Reimplement constant acceleration groups

[alexxy/gromacs.git] / src / gromacs / mdlib / tests / leapfrogtestdata.cpp

diff --git a/src/gromacs/mdlib/tests/leapfrogtestdata.cpp b/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
index e68b893a6b55f99bfde257b1c2c5f82e1cefd57d..cf80cda412530db1c9f349f97979d534dc18b612 100644 (file)
--- a/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
+++ b/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -67,7 +67,12 @@ namespace gmx
 namespace test
 {
 
-LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0, int numTCoupleGroups, int nstpcouple) :
+LeapFrogTestData::LeapFrogTestData(int        numAtoms,
+                                   real       timestep,
+                                   const rvec v0,
+                                   const rvec f0,
+                                   int        numTCoupleGroups,
+                                   int        nstpcouple) :
     numAtoms_(numAtoms),
     timestep_(timestep),
     x0_(numAtoms),
@@ -78,6 +83,7 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
     f_(numAtoms),
     inverseMasses_(numAtoms),
     inverseMassesPerDim_(numAtoms),
+    kineticEnergyData_(numTCoupleGroups == 0 ? 1 : numTCoupleGroups, 0.0, 1),
     numTCoupleGroups_(numTCoupleGroups)
 {
     mdAtoms_.nr = numAtoms_;
@@ -85,9 +91,9 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
     for (int i = 0; i < numAtoms_; i++)
     {
         // Typical PBC box size is tens of nanometers
-        x_[i][XX] = (i%21)*1.0;
-        x_[i][YY] = 6.5 + (i%13)*(-1.0);
-        x_[i][ZZ] = (i%32)*(0.0);
+        x_[i][XX] = (i % 21) * 1.0;
+        x_[i][YY] = 6.5 + (i % 13) * (-1.0);
+        x_[i][ZZ] = (i % 32) * (0.0);
 
         for (int d = 0; d < DIM; d++)
         {
@@ -101,7 +107,7 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
             v0_[i][d] = v_[i][d];
         }
         // Atom masses are ~1-100 g/mol
-        inverseMasses_[i] = 1.0/(1.0 + i%100);
+        inverseMasses_[i] = 1.0 / (1.0 + i % 100);
         for (int d = 0; d < DIM; d++)
         {
             inverseMassesPerDim_[i][d] = inverseMasses_[i];
@@ -118,34 +124,32 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
 
     if (numTCoupleGroups_ == 0)
     {
-        inputRecord_.etc = etcNO;
+        inputRecord_.etc = TemperatureCoupling::No;
         for (int i = 0; i < numAtoms_; i++)
         {
             mdAtoms_.cTC[i] = 0;
         }
-        kineticEnergyData_.ngtc = 1;
         t_grp_tcstat temperatureCouplingGroupData;
         temperatureCouplingGroupData.lambda = 1.0;
-        kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+        kineticEnergyData_.tcstat[0]        = temperatureCouplingGroupData;
     }
     else
     {
-        inputRecord_.etc = etcYES;
+        inputRecord_.etc = TemperatureCoupling::Yes;
         for (int i = 0; i < numAtoms_; i++)
         {
             mdAtoms_.cTC[i] = i % numTCoupleGroups_;
         }
-        kineticEnergyData_.ngtc = numTCoupleGroups_;
-        for (int i = 0; i < numTCoupleGroups; i++)
+        for (int i = 0; i < numTCoupleGroups_; i++)
         {
-            real         tCoupleLambda = 1.0 - (i + 1.0)/10.0;
+            real         tCoupleLambda = 1.0 - (i + 1.0) / 10.0;
             t_grp_tcstat temperatureCouplingGroupData;
             temperatureCouplingGroupData.lambda = tCoupleLambda;
-            kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
+            kineticEnergyData_.tcstat[i]        = temperatureCouplingGroupData;
         }
     }
 
-    inputRecord_.eI      = eiMD;
+    inputRecord_.eI      = IntegrationAlgorithm::MD;
     inputRecord_.delta_t = timestep_;
 
     state_.flags = 0;
@@ -162,29 +166,25 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
     state_.box[ZZ][YY] = 0.0;
     state_.box[ZZ][ZZ] = 10.0;
 
-    kineticEnergyData_.bNEMD            = false;
-    kineticEnergyData_.cosacc.cos_accel = 0.0;
-
-    kineticEnergyData_.nthreads = 1;
-    snew(kineticEnergyData_.ekin_work_alloc, kineticEnergyData_.nthreads);
-    snew(kineticEnergyData_.ekin_work, kineticEnergyData_.nthreads);
-    snew(kineticEnergyData_.dekindl_work, kineticEnergyData_.nthreads);
-
     mdAtoms_.homenr                   = numAtoms_;
     mdAtoms_.haveVsites               = false;
     mdAtoms_.havePartiallyFrozenAtoms = false;
     mdAtoms_.cFREEZE                  = nullptr;
+    mdAtoms_.ptype                    = nullptr;
 
-    update_ = std::make_unique<Update>(&inputRecord_, nullptr);
-    update_->setNumAtoms(numAtoms);
+    update_ = std::make_unique<Update>(inputRecord_, nullptr);
+    update_->updateAfterPartition(numAtoms,
+                                  gmx::ArrayRef<const unsigned short>(),
+                                  gmx::arrayRefFromArray(mdAtoms_.cTC, mdAtoms_.nr),
+                                  gmx::ArrayRef<const unsigned short>());
 
     doPressureCouple_ = (nstpcouple != 0);
 
     if (doPressureCouple_)
     {
-        inputRecord_.epc        = epcPARRINELLORAHMAN;
+        inputRecord_.epc        = PressureCoupling::ParrinelloRahman;
         inputRecord_.nstpcouple = nstpcouple;
-        dtPressureCouple_       = inputRecord_.nstpcouple*inputRecord_.delta_t;
+        dtPressureCouple_       = inputRecord_.nstpcouple * inputRecord_.delta_t;
 
         velocityScalingMatrix_[XX][XX] = 1.2;
         velocityScalingMatrix_[XX][YY] = 0.0;
@@ -200,7 +200,7 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
     }
     else
     {
-        inputRecord_.epc               = epcNO;
+        inputRecord_.epc               = PressureCoupling::No;
         velocityScalingMatrix_[XX][XX] = 1.0;
         velocityScalingMatrix_[XX][YY] = 0.0;
         velocityScalingMatrix_[XX][ZZ] = 0.0;
@@ -213,7 +213,6 @@ LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, c
         velocityScalingMatrix_[ZZ][YY] = 0.0;
         velocityScalingMatrix_[ZZ][ZZ] = 1.0;
     }
-
 }
 
 LeapFrogTestData::~LeapFrogTestData()
@@ -221,5 +220,5 @@ LeapFrogTestData::~LeapFrogTestData()
     sfree(mdAtoms_.cTC);
 }
 
-}  // namespace test
-}  // namespace gmx
+} // namespace test
+} // namespace gmx