Introduce GTest regression tests for replica exchange

This introduces regression tests within the GTest framework for
replica exchange simulations. These tests are restricted to 4
MPI ranks, used as either 2 replicas with 2 ranks each (using
the DD code path), or 4 replicas with 1 rank each (using code
paths used by multiple replicas). As the reference data would
be different for each combination of number of ranks / number
of simulations, this is restricted to a few setups to keep the
reference data manageable.

The tests are run with integrator `md` using v-rescale and
Nose-Hoover thermostats and c-rescale and parrinello-rahman
barostats, covering the thermodynamically correct temperature
and pressure control algorithms. The tests are also run with
integrator `md-vv`, Nose-Hoover thermostat and no barostat
to cover the Trotter decomposition code path (MTTK barostat
would require a different system because it doesn't work
with constraints, and it's not obvious that it would actually
increase code coverage significantly).

Refs #3918

diff --git a/src/programs/mdrun/tests/multisimtest.cpp b/src/programs/mdrun/tests/multisimtest.cpp
index ae612c3b5ffd6fef5bb346b1191f114d16d7e14e..26e5de90b52d421e1d730c1b906a3c69433b7d4d 100644 (file)
--- a/src/programs/mdrun/tests/multisimtest.cpp
+++ b/src/programs/mdrun/tests/multisimtest.cpp
@@ -122,7 +122,8 @@ void MultiSimTest::organizeMdpFile(SimulationRunner*    runner,
                                    IntegrationAlgorithm integrator,
                                    TemperatureCoupling  tcoupl,
                                    PressureCoupling     pcoupl,
-                                   int                  numSteps) const
+                                   int                  numSteps,
+                                   bool                 doRegression) const
 {
     GMX_RELEASE_ASSERT(mpiSetupValid(), "Creating the mdp file without valid MPI setup is useless.");
     const real  baseTemperature = 298;
@@ -138,12 +139,24 @@ void MultiSimTest::organizeMdpFile(SimulationRunner*    runner,
             "tau-t = 1\n"
             "ref-t = %f\n"
             // pressure coupling (if active)
-            "tau-p = 1\n"
+            "tau-p = 2\n"
             "ref-p = %f\n"
             "compressibility = 4.5e-5\n"
             // velocity generation
             "gen-vel = yes\n"
-            "gen-temp = %f\n",
+            "gen-temp = %f\n"
+            "gen-seed = %d\n"
+            // v-rescale and c-rescale use ld-seed
+            "ld-seed = %d\n"
+            // Two systems are used: spc2    non-interacting also at cutoff 1nm
+            //                       tip3p5  has box length of 1.86
+            "rcoulomb = 0.7\n"
+            "rvdw = 0.7\n"
+            // Trajectory output if required
+            "nstxout = %d\n"
+            "nstvout = %d\n"
+            "nstfout = %d\n"
+            "nstenergy = %d\n",
             enumValueToString(integrator),
             enumValueToString(tcoupl),
             enumValueToString(pcoupl),
@@ -155,11 +168,24 @@ void MultiSimTest::organizeMdpFile(SimulationRunner*    runner,
                starting PE decreases on the first step more for the
                replicas with higher number, which will tend to force
                replica exchange to occur. */
-            std::max(baseTemperature - 10 * rank_, real(0)));
+            std::max(baseTemperature - 10 * rank_, real(0)),
+            // If we do regression, we need reproducible velocity
+            // generation, which can be different per simulation
+            (doRegression ? 671324 + simulationNumber_ : -1),
+            // If we do regression, we need reproducible temperature and
+            // pressure coupling, which can be different per simulation
+            (doRegression ? 51203 + simulationNumber_ : -1),
+            // If we do regression, write one intermediate point
+            (doRegression ? int(numSteps / 2) : 0),
+            (doRegression ? int(numSteps / 2) : 0),
+            (doRegression ? int(numSteps / 2) : 0),
+            // If we do regression, print energies every step so
+            // we're sure to catch the replica exchange steps
+            (doRegression ? 1 : 1000));
     runner->useStringAsMdpFile(mdpFileContents);
 }
 
-void MultiSimTest::runGrompp(SimulationRunner* runner, int numSteps) const
+void MultiSimTest::runGrompp(SimulationRunner* runner, int numSteps, bool doRegression, int maxWarnings) const
 {
     // Call grompp once per simulation
     if (rank_ % numRanksPerSimulation_ == 0)
@@ -167,8 +193,10 @@ void MultiSimTest::runGrompp(SimulationRunner* runner, int numSteps) const
         const auto& simulator = std::get<1>(GetParam());
         const auto& tcoupl    = std::get<2>(GetParam());
         const auto& pcoupl    = std::get<3>(GetParam());
-        organizeMdpFile(runner, simulator, tcoupl, pcoupl, numSteps);
-        EXPECT_EQ(0, runner->callGromppOnThisRank());
+        organizeMdpFile(runner, simulator, tcoupl, pcoupl, numSteps, doRegression);
+        CommandLine caller;
+        caller.addOption("-maxwarn", maxWarnings);
+        EXPECT_EQ(0, runner->callGromppOnThisRank(caller));
     }
 
 #if GMX_LIB_MPI

diff --git a/src/programs/mdrun/tests/multisimtest.h b/src/programs/mdrun/tests/multisimtest.h
index 72d713a3f75469d98100aa363984a0a558f24c12..42d4f6bc0b3b7380a2f17013a2d35531dfd72315 100644 (file)
--- a/src/programs/mdrun/tests/multisimtest.h
+++ b/src/programs/mdrun/tests/multisimtest.h
@@ -120,21 +120,27 @@ public:
      * \param tcoupl      Value for the mdp option `tcoupl`
      * \param pcoupl      Value for the mdp option `pcoupl`
      * \param numSteps    Number of MD steps to perform.
+     * \param doRegression  Whether the mdp file will be used for
+     *                      regression tests, request use of
+     *                      reproducible parameters
      */
     void organizeMdpFile(SimulationRunner*    runner,
                          IntegrationAlgorithm integrator,
                          TemperatureCoupling  tcoupl,
                          PressureCoupling     pcoupl,
-                         int                  numSteps) const;
+                         int                  numSteps,
+                         bool                 doRegression) const;
 
     /*! \brief Run grompp on the ranks that need to run it
      *
      * Adds an MPI barrier to ensure that all ranks have written before returning
      *
-     * \param runner    The simulation runner to run grompp on
-     * \param numSteps  Number of MD steps to perform
+     * \param runner        The simulation runner to run grompp on
+     * \param numSteps      Number of MD steps to perform
+     * \param doRegression  Whether to write trajectories during the simulation
+     * \param maxWarnings   Number of grompp warning tolerated
      */
-    void runGrompp(SimulationRunner* runner, int numSteps = 2) const;
+    void runGrompp(SimulationRunner* runner, int numSteps = 2, bool doRegression = false, int maxWarnings = 0) const;
     //! Test that a basic simulation works
     void runExitsNormallyTest();
     //! Test that mdrun -maxh and restart works

diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..73948df
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_d.xml
@@ -0,0 +1,3398 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Simulation Name="Replica 0">
+    <ReplExOutput Name="Output">
+      <String Name="Replica Exchange Output"><![CDATA[
+Repl  There are 4 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
+Replica exchange at step 4 time 0.00400
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange at step 8 time 0.00800
+Repl ex  0    1 x  2    3
+Repl pr        1.0     
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
+Repl     0    1    2    3
+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
+Repl     0    1    2    3
+Repl        2    1    2
+Repl  average number of exchanges:
+Repl     0    1    2    3
+Repl      1.0  1.0  1.0
+Repl                Empirical Transition Matrix
+Repl       1       2       3       4
+Repl  0.3333  0.6667  0.0000  0.0000  0
+Repl  0.6667  0.0000  0.3333  0.0000  1
+Repl  0.0000  0.3333  0.0000  0.6667  2
+Repl  0.0000  0.0000  0.6667  0.3333  3
+]]></String>
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+Repl  There are 4 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98715
+Replica exchange information below: ex and x = exchange, pr = probability
+Replica exchange at step 4 time 0.00400
+Repl 2 <-> 3  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange at step 8 time 0.00800
+Repl 1 <-> 2  [ not checked ]
+Repl ex  0    1 x  2    3
+Repl pr        1.0     
+Replica exchange at step 12 time 0.01200
+Repl 2 <-> 3  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
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+Repl  average number of exchanges:
+Repl     0    1    2    3
+Repl      1.0  1.0  1.0
+Repl                Empirical Transition Matrix
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..824db16
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_1RanksPerSimulation_s.xml
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+Replica-exchange molecular dynamics method for protein folding
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
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+Replica random seed: 98715
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+Repl 2 <-> 3  [ not checked ]
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+Repl ex  0    1 x  2    3
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+Repl 2 <-> 3  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..b0cffec
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_d.xml
@@ -0,0 +1,1696 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Simulation Name="Replica 0">
+    <ReplExOutput Name="Output">
+      <String Name="Replica Exchange Output"><![CDATA[
+Repl  There are 2 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.02
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
+Replica exchange at step 4 time 0.00400
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange at step 8 time 0.00800
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..cde2d0f
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_Crescale_4Ranks_2RanksPerSimulation_s.xml
@@ -0,0 +1,1696 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica random seed: 98713
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+Repl 0 <-> 1  [ not checked ]
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+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..a9d603d
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml
@@ -0,0 +1,3398 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
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+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
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+Repl                Empirical Transition Matrix
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..47b9bae
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml
@@ -0,0 +1,3398 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
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+Replica random seed: 98716
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+Repl 2 <-> 3  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..0e5e475
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml
@@ -0,0 +1,1696 @@
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..6ef1628
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_NoseHoover_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml
@@ -0,0 +1,1696 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.02
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
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+Repl pr      
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0
+Repl  number of exchanges:
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+Repl        2
+Repl  average number of exchanges:
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+Repl      1.0
+Repl        Empirical Transition Matrix
+Repl       1       2
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+Repl  0.6667  0.3333  1
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..76f042c
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_d.xml
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
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+Repl 2 <-> 3  [ not checked ]
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..fe0f94e
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_1RanksPerSimulation_s.xml
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+Replica-exchange molecular dynamics method for protein folding
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+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
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+Replica random seed: 98715
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+Repl 2 <-> 3  [ not checked ]
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+Repl pr   1.0       1.0
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..859158c
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_d.xml
@@ -0,0 +1,1696 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <Simulation Name="Replica 0">
+    <ReplExOutput Name="Output">
+      <String Name="Replica Exchange Output"><![CDATA[
+Repl  There are 2 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.02
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
+Replica exchange at step 4 time 0.00400
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange at step 8 time 0.00800
+Repl ex  0    1
+Repl pr      
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
+Repl     0    1
+Repl      1.0
+Repl  number of exchanges:
+Repl     0    1
+Repl        2
+Repl  average number of exchanges:
+Repl     0    1
+Repl      1.0
+Repl        Empirical Transition Matrix
+Repl       1       2
+Repl  0.3333  0.6667  0
+Repl  0.6667  0.3333  1
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..70c1b3a
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_Crescale_4Ranks_2RanksPerSimulation_s.xml
@@ -0,0 +1,1696 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica random seed: 98713
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+Replica exchange statistics
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..5773e57
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_d.xml
@@ -0,0 +1,3398 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
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+Repl pr   1.0       1.0
+Replica exchange statistics
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..932022b
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_1RanksPerSimulation_s.xml
@@ -0,0 +1,3398 @@
+<?xml version="1.0"?>
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+Repl  There are 4 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.01  1.02  1.03
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl pr   1.0       1.0
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+Repl pr        1.0     
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
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+Repl        2    1    2
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+Repl      1.0  1.0  1.0
+Repl                Empirical Transition Matrix
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+Repl  0.0000  0.3333  0.0000  0.6667  2
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+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..2c46cdd
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_d.xml
@@ -0,0 +1,1696 @@
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+Replica-exchange molecular dynamics method for protein folding
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+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
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+Replica random seed: 98713
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+Replica exchange statistics
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..0d53661
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceLeapFrog_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_md_Vrescale_ParrinelloRahman_4Ranks_2RanksPerSimulation_s.xml
@@ -0,0 +1,1696 @@
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+Replica-exchange molecular dynamics method for protein folding
+Repl  Using Constant Pressure REMD.
+Replica-exchange {M}onte {C}arlo method for the isobaric-isothermal ensemble
+Replica exchange in temperature
+Repl  p  1.00  1.02
+Replica exchange interval: 4
+Replica random seed: 98713
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+Repl pr      
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange statistics
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+Repl      1.0
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+Repl        2
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+Repl  0.6667  0.3333  1
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..8ba3904
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_d.xml
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
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+Replica random seed: 98714
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98715
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 2 <-> 3  [ not checked ]
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+Replica-exchange molecular dynamics method for protein folding
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+Replica random seed: 98716
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..e106cd3
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_1RanksPerSimulation_s.xml
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+Replica-exchange molecular dynamics method for protein folding
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98714
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange at step 8 time 0.00800
+Repl 1 <-> 2  [ not checked ]
+Repl ex  0    1 x  2    3
+Repl pr        1.0     
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1    2 x  3
+Repl pr   1.0       1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
+Repl     0    1    2    3
+Repl      1.0  1.0  1.0
+Repl  number of exchanges:
+Repl     0    1    2    3
+Repl        2    1    2
+Repl  average number of exchanges:
+Repl     0    1    2    3
+Repl      1.0  1.0  1.0
+Repl                Empirical Transition Matrix
+Repl       1       2       3       4
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+Repl  0.6667  0.0000  0.3333  0.0000  1
+Repl  0.0000  0.3333  0.0000  0.6667  2
+Repl  0.0000  0.0000  0.6667  0.3333  3
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98715
+Replica exchange information below: ex and x = exchange, pr = probability
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
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+Replica random seed: 98716
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_d.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_d.xml
new file mode 100644 (file)
index 0000000..b4b73af
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_d.xml
@@ -0,0 +1,1690 @@
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
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+Repl pr      
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange statistics
+Repl  3 attempts, 2 odd, 1 even
+Repl  average probabilities:
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+Repl      1.0
+Repl  number of exchanges:
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+Repl        2
+Repl  average number of exchanges:
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+Repl        Empirical Transition Matrix
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+Repl  0.3333  0.6667  0
+Repl  0.6667  0.3333  1
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diff --git a/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_s.xml b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_s.xml
new file mode 100644 (file)
index 0000000..3b02adf
--- /dev/null
+++ b/src/programs/mdrun/tests/refdata/ReplicaExchangeIsEquivalentToReferenceVelocityVerlet_ReplicaExchangeRegressionTest_WithinTolerances_ReplExRegression_mdvv_NoseHoover_No_4Ranks_2RanksPerSimulation_s.xml
@@ -0,0 +1,1690 @@
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+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98713
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl  There are 2 replicas:
+Replica-exchange molecular dynamics method for protein folding
+Replica exchange in temperature
+Replica exchange interval: 4
+Replica random seed: 98714
+Replica exchange information below: ex and x = exchange, pr = probability
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+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
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+Repl ex  0    1
+Repl pr      
+Replica exchange at step 12 time 0.01200
+Repl 0 <-> 1  [ not checked ]
+Repl ex  0 x  1
+Repl pr   1.0
+Replica exchange statistics
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+Repl      1.0
+Repl  number of exchanges:
+Repl     0    1
+Repl        2
+Repl  average number of exchanges:
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+Repl      1.0
+Repl        Empirical Transition Matrix
+Repl       1       2
+Repl  0.3333  0.6667  0
+Repl  0.6667  0.3333  1
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+        <Real Name="X">-35.901039</Real>
+        <Real Name="Y">16.905447</Real>
+        <Real Name="Z">54.424404</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-258.07733</Real>
+        <Real Name="Y">-52.450287</Real>
+        <Real Name="Z">175.90759</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">212.8786</Real>
+        <Real Name="Y">26.47406</Real>
+        <Real Name="Z">-197.02202</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">96.675217</Real>
+        <Real Name="Y">33.097923</Real>
+        <Real Name="Z">-53.513664</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-59.61908</Real>
+        <Real Name="Y">-231.46751</Real>
+        <Real Name="Z">9.0253601</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-26.94574</Real>
+        <Real Name="Y">75.055931</Real>
+        <Real Name="Z">-11.075729</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-78.221039</Real>
+        <Real Name="Y">70.167076</Real>
+        <Real Name="Z">213.2876</Real>
+      </Vector>
+    </Sequence>
+    <Real Name="Time 0.016000 Step 16 Box[0][0]">1.86206</Real>
+    <Real Name="Time 0.016000 Step 16 Box[0][1]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[0][2]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[1][0]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[1][1]">1.86206</Real>
+    <Real Name="Time 0.016000 Step 16 Box[1][2]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[2][0]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[2][1]">0</Real>
+    <Real Name="Time 0.016000 Step 16 Box[2][2]">1.86206</Real>
+    <Sequence Name="Time 0.016000 Step 16 X">
+      <Int Name="Length">15</Int>
+      <Vector>
+        <Real Name="X">0.0014099475</Real>
+        <Real Name="Y">0.58940381</Real>
+        <Real Name="Z">0.24167866</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.8540177</Real>
+        <Real Name="Y">0.67624474</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">0.075623721</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">0.98185748</Real>
+        <Real Name="Y">0.62914616</Real>
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+      </Vector>
+      <Vector>
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+      </Vector>
+      <Vector>
+        <Real Name="X">0.94000816</Real>
+        <Real Name="Y">0.71004111</Real>
+        <Real Name="Z">1.5421597</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.3893729</Real>
+        <Real Name="Y">0.44759429</Real>
+        <Real Name="Z">1.1803213</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.3376812</Real>
+        <Real Name="Y">0.47841489</Real>
+        <Real Name="Z">1.254755</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.3266979</Real>
+        <Real Name="Y">0.40042442</Real>
+        <Real Name="Z">1.1254655</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.6489143</Real>
+        <Real Name="Y">0.3180455</Real>
+        <Real Name="Z">0.29607984</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.7082195</Real>
+        <Real Name="Y">0.34094101</Real>
+        <Real Name="Z">0.22451863</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.6021434</Real>
+        <Real Name="Y">0.24066503</Real>
+        <Real Name="Z">0.2646623</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.7750171</Real>
+        <Real Name="Y">0.39916423</Real>
+        <Real Name="Z">0.020688197</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.7156733</Real>
+        <Real Name="Y">0.4075307</Real>
+        <Real Name="Z">1.8081114</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.7890438</Real>
+        <Real Name="Y">0.48907131</Real>
+        <Real Name="Z">0.050391514</Real>
+      </Vector>
+    </Sequence>
+    <Sequence Name="Time 0.016000 Step 16 V">
+      <Int Name="Length">15</Int>
+      <Vector>
+        <Real Name="X">-0.20774576</Real>
+        <Real Name="Y">-0.57286853</Real>
+        <Real Name="Z">-0.34285799</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">0.33856916</Real>
+        <Real Name="Y">-1.4004967</Real>
+        <Real Name="Z">1.6255525</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">2.4273114</Real>
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+        <Real Name="Z">2.896225</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">0.42057839</Real>
+        <Real Name="Y">-0.10071245</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">1.570209</Real>
+        <Real Name="Y">0.80972606</Real>
+        <Real Name="Z">0.24616064</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">1.5919843</Real>
+        <Real Name="Y">0.45125833</Real>
+        <Real Name="Z">0.013387703</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-0.52939558</Real>
+        <Real Name="Y">0.024729343</Real>
+        <Real Name="Z">0.37319544</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">0.56629837</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">-0.94382876</Real>
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+        <Real Name="Z">2.3638034</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">0.23067445</Real>
+        <Real Name="Y">0.30649024</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">0.3907373</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">0.8242712</Real>
+        <Real Name="Y">0.30516517</Real>
+        <Real Name="Z">-1.282984</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-0.19892913</Real>
+        <Real Name="Y">0.37591052</Real>
+        <Real Name="Z">-0.25146261</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">0.49795806</Real>
+        <Real Name="Y">0.010643594</Real>
+        <Real Name="Z">-0.84650415</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-2.7428274</Real>
+        <Real Name="Y">0.28813386</Real>
+        <Real Name="Z">1.2155147</Real>
+      </Vector>
+    </Sequence>
+    <Sequence Name="Time 0.016000 Step 16 F">
+      <Int Name="Length">15</Int>
+      <Vector>
+        <Real Name="X">-71.80658</Real>
+        <Real Name="Y">68.801941</Real>
+        <Real Name="Z">-364.28366</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">3.7374649</Real>
+        <Real Name="Y">-0.12477875</Real>
+        <Real Name="Z">112.0171</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">136.45911</Real>
+        <Real Name="Y">2.7420578</Real>
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+      </Vector>
+      <Vector>
+        <Real Name="X">23.638466</Real>
+        <Real Name="Y">-23.618427</Real>
+        <Real Name="Z">-37.764069</Real>
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+      <Vector>
+        <Real Name="X">-5.6398582</Real>
+        <Real Name="Y">7.0323143</Real>
+        <Real Name="Z">14.355347</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-9.3168449</Real>
+        <Real Name="Y">12.807716</Real>
+        <Real Name="Z">11.920631</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">34.758224</Real>
+        <Real Name="Y">-3.9805069</Real>
+        <Real Name="Z">-32.326981</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-60.161064</Real>
+        <Real Name="Y">9.1062698</Real>
+        <Real Name="Z">-17.994423</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-13.121216</Real>
+        <Real Name="Y">4.248909</Real>
+        <Real Name="Z">18.122276</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-316.19507</Real>
+        <Real Name="Y">-133.0134</Real>
+        <Real Name="Z">276.64075</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">244.08429</Real>
+        <Real Name="Y">103.30573</Real>
+        <Real Name="Z">-285.05554</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">118.7437</Real>
+        <Real Name="Y">60.946838</Real>
+        <Real Name="Z">-64.615013</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-73.573181</Real>
+        <Real Name="Y">-317.42291</Real>
+        <Real Name="Z">-33.423706</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">19.039402</Real>
+        <Real Name="Y">56.988865</Real>
+        <Real Name="Z">25.400909</Real>
+      </Vector>
+      <Vector>
+        <Real Name="X">-30.646835</Real>
+        <Real Name="Y">152.17938</Real>
+        <Real Name="Z">240.38171</Real>
+      </Vector>
+    </Sequence>
+  </Simulation>
+</ReferenceData>

diff --git a/src/programs/mdrun/tests/replicaexchange.cpp b/src/programs/mdrun/tests/replicaexchange.cpp
index 081d924348736dee3fbceb5d061c000137ae05c4..e704e78b8add02fd138c8942ed60851cea500262 100644 (file)
--- a/src/programs/mdrun/tests/replicaexchange.cpp
+++ b/src/programs/mdrun/tests/replicaexchange.cpp
@@ -45,15 +45,23 @@
 
 #include "config.h"
 
+#include <regex>
+
 #include <gtest/gtest.h>
 
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/filestream.h"
 #include "gromacs/utility/path.h"
 #include "gromacs/utility/stringutil.h"
 
+#include "testutils/refdata.h"
 #include "testutils/testfilemanager.h"
 
+#include "energycomparison.h"
 #include "multisimtest.h"
+#include "trajectorycomparison.h"
 
 namespace gmx
 {
@@ -105,5 +113,241 @@ INSTANTIATE_TEST_CASE_P(InNvt,
                                            ::testing::Values(IntegrationAlgorithm::MD),
                                            ::testing::Values(TemperatureCoupling::VRescale),
                                            ::testing::Values(PressureCoupling::No)));
+
+/*! \brief Return replica exchange related output from logfile
+ *
+ * All replica exchange related output in log files start with 'Repl',
+ * making extraction easy. This function also removes the printing of
+ * energy differences, as the log files are compared exactly, and
+ * energy differences will slightly vary between runs.
+ *
+ * \param logFileName  Name of log file
+ * \return  Replica exchange related output in log file
+ */
+static std::string getReplicaExchangeOutputFromLogFile(const std::string& logFileName)
+{
+    TextInputFile logFile(logFileName);
+    std::string   replExOutput;
+    std::string   line;
+    while (logFile.readLine(&line))
+    {
+        // All replica exchange output lines starts with "Repl"
+        if (startsWith(line, "Repl"))
+        {
+            // This is an exact comparison, so we can't compare the energies which
+            // are slightly different per run. Energies are tested later.
+            const auto pos = line.find("dE_term");
+            if (pos != std::string::npos)
+            {
+                line.replace(line.begin() + pos, line.end(), "[ not checked ]\n");
+            }
+            replExOutput.append(line);
+        }
+    }
+    return replExOutput;
+}
+
+//! Convenience typedef
+typedef MultiSimTest ReplicaExchangeRegressionTest;
+
+/* Run replica exchange simulations, compare to reference data
+ *
+ * Reference data generated by
+ *
+ * GROMACS version:    2022-dev
+ * Precision:          single and double (separate reference data)
+ * Memory model:       64 bit
+ * MPI library:        MPI
+ * OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
+ * GPU support:        disabled
+ * SIMD instructions:  AVX2_256
+ * FFT library:        fftw-3.3.9-sse2-avx
+ * RDTSCP usage:       enabled
+ * TNG support:        enabled
+ * Hwloc support:      disabled
+ * Tracing support:    disabled
+ * C compiler:         /usr/local/bin/mpicc Clang 8.0.1
+ * C++ compiler:       /usr/local/bin/mpic++ Clang 8.0.1
+ *
+ */
+TEST_P(ReplicaExchangeRegressionTest, WithinTolerances)
+{
+    if (!mpiSetupValid())
+    {
+        // Can't test multi-sim without multiple simulations
+        return;
+    }
+
+    if (size_ != 4)
+    {
+        // Results are depending on number of ranks, and we can't have reference
+        // data for all cases. Restricting the regression tests to runs with 4 ranks.
+        // This allows testing 4 replicas with single rank, or 2 replicas with 2 ranks each.
+        return;
+    }
+    const auto& tcoupl = std::get<2>(GetParam());
+    const auto& pcoupl = std::get<3>(GetParam());
+
+    const int numSteps       = 16;
+    const int exchangePeriod = 4;
+    // grompp warns about generating velocities and using parrinello-rahman
+    const int maxWarnings = (pcoupl == PressureCoupling::ParrinelloRahman ? 1 : 0);
+
+    mdrunCaller_->addOption("-replex", exchangePeriod);
+    // Seeds need to be reproducible for regression, but can be different per simulation
+    mdrunCaller_->addOption("-reseed", 98713 + simulationNumber_);
+
+    SimulationRunner runner(&fileManager_);
+    runner.useTopGroAndNdxFromDatabase("tip3p5");
+
+    runGrompp(&runner, numSteps, true, maxWarnings);
+    ASSERT_EQ(0, runner.callMdrun(*mdrunCaller_));
+
+#if GMX_LIB_MPI
+    // Make sure all simulations are finished before checking the results.
+    MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+
+    // We only test simulation results on one rank to avoid problems with reference file access.
+    if (rank_ == 0)
+    {
+        // Create reference data helper object
+        TestReferenceData refData;
+
+        // Specify how energy trajectory comparison must work
+        const auto hasConservedField =
+                !(tcoupl == TemperatureCoupling::No && pcoupl == PressureCoupling::No);
+        // Tolerances copied from simulator tests
+        EnergyTermsToCompare energyTermsToCompare{ {
+                { interaction_function[F_EPOT].longname,
+                  relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+                { interaction_function[F_EKIN].longname,
+                  relativeToleranceAsPrecisionDependentUlp(60.0, 200, 160) },
+                { interaction_function[F_PRES].longname,
+                  relativeToleranceAsPrecisionDependentFloatingPoint(10.0, 0.01, 0.001) },
+        } };
+        if (hasConservedField)
+        {
+            energyTermsToCompare.emplace(interaction_function[F_ECONSERVED].longname,
+                                         relativeToleranceAsPrecisionDependentUlp(50.0, 100, 80));
+        }
+
+        // Specify how trajectory frame matching must work.
+        const TrajectoryFrameMatchSettings trajectoryMatchSettings{ true,
+                                                                    true,
+                                                                    true,
+                                                                    ComparisonConditions::MustCompare,
+                                                                    ComparisonConditions::MustCompare,
+                                                                    ComparisonConditions::MustCompare,
+                                                                    MaxNumFrames::compareAllFrames() };
+        TrajectoryTolerances trajectoryTolerances = TrajectoryComparison::s_defaultTrajectoryTolerances;
+        // By default, velocity tolerance is MUCH tighter than force tolerance
+        trajectoryTolerances.velocities = trajectoryTolerances.forces;
+        // Build the functor that will compare reference and test
+        // trajectory frames in the chosen way.
+        TrajectoryComparison trajectoryComparison{ trajectoryMatchSettings, trajectoryTolerances };
+
+        // Loop over simulations
+        for (int simulationNumber = 0; simulationNumber < (size_ / numRanksPerSimulation_);
+             simulationNumber++)
+        {
+            TestReferenceChecker simulationChecker(refData.rootChecker().checkCompound(
+                    "Simulation", formatString("Replica %d", simulationNumber)));
+
+            const auto logFileName =
+                    std::regex_replace(runner.logFileName_,
+                                       std::regex(formatString("sim_%d", simulationNumber_)),
+                                       formatString("sim_%d", simulationNumber));
+            const auto energyFileName =
+                    std::regex_replace(runner.edrFileName_,
+                                       std::regex(formatString("sim_%d", simulationNumber_)),
+                                       formatString("sim_%d", simulationNumber));
+            const auto trajectoryFileName =
+                    std::regex_replace(runner.fullPrecisionTrajectoryFileName_,
+                                       std::regex(formatString("sim_%d", simulationNumber_)),
+                                       formatString("sim_%d", simulationNumber));
+
+            // Check log replica exchange related output (contains exchange statistics)
+            auto replicaExchangeOutputChecker =
+                    simulationChecker.checkCompound("ReplExOutput", "Output");
+            const auto replExOutput = getReplicaExchangeOutputFromLogFile(logFileName);
+            replicaExchangeOutputChecker.checkTextBlock(replExOutput, "Replica Exchange Output");
+
+            // Check that the energies agree with the refdata within tolerance.
+            checkEnergiesAgainstReferenceData(energyFileName, energyTermsToCompare, &simulationChecker);
+
+            // Check that the trajectories agree with the refdata within tolerance.
+            checkTrajectoryAgainstReferenceData(trajectoryFileName, trajectoryComparison, &simulationChecker);
+
+        } // end loop over simulations
+    }     // end testing simulations on one rank
+
+#if GMX_LIB_MPI
+    // Make sure testing is complete before returning - ranks delete temporary files on exit
+    MPI_Barrier(MdrunTestFixtureBase::communicator_);
+#endif
+}
+
+/*! \brief Helper struct printing custom test name
+ *
+ * Regression test results not only depend on the test parameters, but
+ * also on the total number of ranks and the precision. Names must
+ * reflect that to identify correct reference data.
+ */
+struct PrintReplicaExchangeParametersToString
+{
+    template<class ParamType>
+    std::string operator()(const testing::TestParamInfo<ParamType>& parameter) const
+    {
+        auto testIdentifier =
+                formatString("ReplExRegression_%s_%s_%s_%dRanks_%dRanksPerSimulation_%s",
+                             enumValueToString(std::get<1>(parameter.param)),
+                             enumValueToString(std::get<2>(parameter.param)),
+                             enumValueToString(std::get<3>(parameter.param)),
+                             gmx_node_num(),
+                             static_cast<int>(std::get<0>(parameter.param)),
+                             GMX_DOUBLE ? "d" : "s");
+        // Valid GTest names cannot include hyphens
+        testIdentifier.erase(std::remove(testIdentifier.begin(), testIdentifier.end(), '-'),
+                             testIdentifier.end());
+        return testIdentifier;
+    }
+};
+
+#if GMX_LIB_MPI
+INSTANTIATE_TEST_CASE_P(
+        ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+        ReplicaExchangeRegressionTest,
+        ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+                           ::testing::Values(IntegrationAlgorithm::MD),
+                           ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+                           ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+        PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_CASE_P(ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+                        ReplicaExchangeRegressionTest,
+                        ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+                                                             NumRanksPerSimulation(2)),
+                                           ::testing::Values(IntegrationAlgorithm::VV),
+                                           ::testing::Values(TemperatureCoupling::NoseHoover),
+                                           ::testing::Values(PressureCoupling::No)),
+                        PrintReplicaExchangeParametersToString());
+#else
+INSTANTIATE_TEST_CASE_P(
+        DISABLED_ReplicaExchangeIsEquivalentToReferenceLeapFrog,
+        ReplicaExchangeRegressionTest,
+        ::testing::Combine(::testing::Values(NumRanksPerSimulation(1), NumRanksPerSimulation(2)),
+                           ::testing::Values(IntegrationAlgorithm::MD),
+                           ::testing::Values(TemperatureCoupling::VRescale, TemperatureCoupling::NoseHoover),
+                           ::testing::Values(PressureCoupling::CRescale, PressureCoupling::ParrinelloRahman)),
+        PrintReplicaExchangeParametersToString());
+INSTANTIATE_TEST_CASE_P(DISABLED_ReplicaExchangeIsEquivalentToReferenceVelocityVerlet,
+                        ReplicaExchangeRegressionTest,
+                        ::testing::Combine(::testing::Values(NumRanksPerSimulation(1),
+                                                             NumRanksPerSimulation(2)),
+                                           ::testing::Values(IntegrationAlgorithm::VV),
+                                           ::testing::Values(TemperatureCoupling::NoseHoover),
+                                           ::testing::Values(PressureCoupling::No)),
+                        PrintReplicaExchangeParametersToString());
+#endif
 } // namespace test
 } // namespace gmx