Merge pull request #333 from GOMC-WSU/revert-332-revert-327-brownian

Revert "Revert "MultiParticle Brownian like motion""

CMake/FileLists.cmake

@@ -42,6 +42,7 @@ set(sources
    src/PDBOutput.cpp
    src/PRNGSetup.cpp
    src/PSFOutput.cpp
+   src/Random123Wrapper.cpp
    src/Reader.cpp
    src/Simulation.cpp
    src/StaticVals.cpp
@@ -131,6 +132,7 @@ set(headers
    src/PRNG.h
    src/PRNGSetup.h
    src/PSFOutput.h
+   src/Random123Wrapper.h
    src/Reader.h
    src/SeedReader.h
    src/Setup.h
@@ -174,6 +176,7 @@ set(headers
    src/moves/MoleculeTransfer.h
    src/moves/MoveBase.h
    src/moves/MultiParticle.h
+   src/moves/MultiParticleBrownianMotion.h
    src/moves/Regrowth.h
    src/moves/Rotation.h
    src/moves/TargetedSwap.h

lib/BasicTypes.h

@@ -123,6 +123,18 @@ struct XYZ {
       return true;
     return false;
   }
+  bool operator<(XYZ const& rhs)
+  {
+    if(x < rhs.x && y < rhs.y && z < rhs.z)
+      return true;
+    return false;
+  }
+  bool operator>(XYZ const& rhs)
+  {
+    if(x > rhs.x || y > rhs.y || z > rhs.z)
+      return true;
+    return false;
+  }
   XYZ& operator+=(XYZ const& rhs)
   {
     x += rhs.x;

src/BoxDimensions.h

@@ -49,6 +49,11 @@ class BoxDimensions
   {
     return axis.Get(b);
   }
+
+  XYZ GetHalfAxis(const uint b) const
+  {
+    return halfAx.Get(b);
+  }
 
   double GetTotVolume(const uint b1, const uint b2) const;
 

src/ConfigSetup.cpp

@@ -76,6 +76,7 @@ ConfigSetup::ConfigSetup(void)
   sys.moves.intraSwap = DBL_MAX;
   sys.moves.multiParticleEnabled = false;
   sys.moves.multiParticle = DBL_MAX;
+  sys.moves.multiParticleBrownian = DBL_MAX;
   sys.moves.regrowth = DBL_MAX;
   sys.moves.crankShaft = DBL_MAX;
   sys.moves.intraMemc = DBL_MAX;
@@ -678,6 +679,14 @@ void ConfigSetup::Init(const char *fileName, MultiSim const*const& multisim)
       printf("%-40s %-4.4f \n",
              "Info: Multi-Particle move frequency",
              sys.moves.multiParticle);
+    } else if(CheckString(line[0], "MultiParticleBrownianFreq")) {
+      sys.moves.multiParticleBrownian = stringtod(line[1]);
+      if(sys.moves.multiParticleBrownian > 0.00) {
+        sys.moves.multiParticleEnabled = true;
+      }
+      printf("%-40s %-4.4f \n",
+             "Info: Multi-Particle Brownian move frequency",
+             sys.moves.multiParticleBrownian);
     } else if(CheckString(line[0], "IntraSwapFreq")) {
       sys.moves.intraSwap = stringtod(line[1]);
       printf("%-40s %-4.4f \n", "Info: Intra-Swap move frequency",
@@ -1251,6 +1260,13 @@ void ConfigSetup::fillDefaults(void)
            sys.moves.multiParticle);
   }
 
+  if(sys.moves.multiParticleBrownian == DBL_MAX) {
+    sys.moves.multiParticleBrownian = 0.000;
+    printf("%-40s %-4.4f \n",
+           "Default: Multi-Particle Brownian move frequency",
+           sys.moves.multiParticleBrownian);
+  }
+
   if(sys.moves.intraMemc == DBL_MAX) {
     sys.moves.intraMemc = 0.0;
     printf("%-40s %-4.4f \n", "Default: Intra-MEMC move frequency",
@@ -1506,6 +1522,12 @@ void ConfigSetup::verifyInputs(void)
     }
   }
   #endif
+  if(abs(sys.moves.multiParticle) > 0.0000001 && 
+    abs(sys.moves.multiParticleBrownian) > 0.0000001) {
+    std::cout << "Error: Both multi-Particle and multi-Particle Brownian! " <<
+    " cannot be used at the same time!" << std::endl;
+    exit(EXIT_FAILURE);
+  }
 
   if(!sys.elect.enable && sys.elect.oneFourScale != DBL_MAX) {
     printf("Warning: 1-4 Electrostatic scaling set, but will be ignored.\n");
@@ -1660,8 +1682,8 @@ void ConfigSetup::verifyInputs(void)
   if(std::abs(sys.moves.displace + sys.moves.rotate + sys.moves.transfer +
               sys.moves.intraSwap + sys.moves.volume + sys.moves.regrowth +
               sys.moves.memc + sys.moves.intraMemc + sys.moves.crankShaft +
-              sys.moves.multiParticle + sys.moves.cfcmc + 
-              sys.moves.targetedSwap - 1.0) > 0.001) {
+              sys.moves.multiParticle + sys.moves.multiParticleBrownian + 
+              sys.moves.cfcmc + sys.moves.targetedSwap - 1.0) > 0.001) {
     std::cout << "Error: Sum of move frequencies is not equal to one!\n";
     exit(EXIT_FAILURE);
   }
@@ -1673,7 +1695,8 @@ void ConfigSetup::verifyInputs(void)
 
   if(std::abs(sys.moves.displace + sys.moves.rotate + sys.moves.intraSwap +
               sys.moves.volume + sys.moves.regrowth + sys.moves.intraMemc +
-              sys.moves.crankShaft + sys.moves.multiParticle - 1.0) > 0.001) {
+              sys.moves.crankShaft + sys.moves.multiParticle +
+              sys.moves.multiParticleBrownian - 1.0) > 0.001) {
     std::cout << "Error: Sum of move frequencies is not equal to one!\n";
     exit(EXIT_FAILURE);
   }
@@ -1686,15 +1709,15 @@ void ConfigSetup::verifyInputs(void)
   if(std::abs(sys.moves.displace + sys.moves.rotate + sys.moves.intraSwap +
               sys.moves.transfer + sys.moves.regrowth + sys.moves.memc +
               sys.moves.intraMemc + sys.moves.crankShaft +
-              sys.moves.multiParticle + sys.moves.cfcmc +
-              sys.moves.targetedSwap - 1.0) > 0.001) {
+              sys.moves.multiParticle + sys.moves.multiParticleBrownian + 
+              sys.moves.cfcmc + sys.moves.targetedSwap - 1.0) > 0.001) {
     std::cout << "Error: Sum of move frequencies is not equal to one!!\n";
     exit(EXIT_FAILURE);
   }
 #else
   if(std::abs(sys.moves.displace + sys.moves.rotate + sys.moves.intraSwap +
               sys.moves.regrowth + sys.moves.intraMemc + sys.moves.crankShaft +
-              sys.moves.multiParticle - 1.0) > 0.001) {
+              sys.moves.multiParticle + sys.moves.multiParticleBrownian - 1.0) > 0.001) {
     std::cout << "Error: Sum of move frequencies is not equal to one!!\n";
     exit(EXIT_FAILURE);
   }

src/ConfigSetup.h

@@ -183,8 +183,8 @@ struct Step {
 //Holds the percentage of each kind of move for this ensemble.
 struct MovePercents {
   double displace, rotate, intraSwap, intraMemc, regrowth, crankShaft,
-         multiParticle;
-  bool multiParticleEnabled;
+         multiParticle, multiParticleBrownian;
+  bool multiParticleEnabled; // for both multiparticle and multiparticleBrownian
 #ifdef VARIABLE_VOLUME
   double volume;
 #endif

src/ConsoleOutput.cpp

@@ -121,6 +121,13 @@ void ConsoleOutput::PrintMove(const uint box, const ulong step) const
       printElement(var->GetAcceptPercent(box, sub), elementWidth);
     }
 
+    if(var->Performed(mv::MULTIPARTICLE_BM)) {
+      sub = mv::MULTIPARTICLE_BM;
+      printElement(var->GetTries(box, sub), elementWidth);
+      printElement(var->GetAccepted(box, sub), elementWidth);
+      printElement(var->GetAcceptPercent(box, sub), elementWidth);
+    }
+
     if(var->Performed(mv::INTRA_SWAP)) {
       sub = mv::INTRA_SWAP;
       printElement(var->GetTries(box, sub), elementWidth);
@@ -371,6 +378,12 @@ void ConsoleOutput::PrintMoveTitle()
     printElement("MPACCEPT%", elementWidth);
   }
 
+  if(var->Performed(mv::MULTIPARTICLE_BM)) {
+    printElement("MULTIPARTICLEBM", elementWidth);
+    printElement("MPBMACCEPT", elementWidth);
+    printElement("MPBMACCEPT%", elementWidth);
+  }
+
   if(var->Performed(mv::INTRA_SWAP)) {
     printElement("INTRASWAP", elementWidth);
     printElement("INTACCEPT", elementWidth);

src/GOMCEventsProfileDef.h

@@ -20,6 +20,7 @@ GOMC_PROFILE_EVENT(FREE_ENERGY_OUTPUT, "free_energy_file")
 GOMC_PROFILE_EVENT(DISPLACE, "translate_move")
 GOMC_PROFILE_EVENT(ROTATE, "rotate_move")
 GOMC_PROFILE_EVENT(MULTIPARTICLE, "multiParticle_move")
+GOMC_PROFILE_EVENT(MULTIPARTICLE_BM, "multiParticleBM_move")
 GOMC_PROFILE_EVENT(INTRA_SWAP, "intraSwap_move")
 GOMC_PROFILE_EVENT(INTRA_MEMC, "intraMEMC_move")
 GOMC_PROFILE_EVENT(CRANKSHAFT, "crankshaft_move")
@@ -33,6 +34,7 @@ GOMC_PROFILE_EVENT(CFCMC, "CFCMC_move")
 GOMC_PROFILE_EVENT(PREP_DISPLACE, "prepare_translate_move")
 GOMC_PROFILE_EVENT(PREP_ROTATE, "prepare_rotate_move")
 GOMC_PROFILE_EVENT(PREP_MULTIPARTICLE, "prepare_multiParticle_move")
+GOMC_PROFILE_EVENT(PREP_MULTIPARTICLE_BM, "prepare_multiParticleBM_move")
 GOMC_PROFILE_EVENT(PREP_INTRA_SWAP, "prepare_intraSwap_move")
 GOMC_PROFILE_EVENT(PREP_INTRA_MEMC, "prepare_intraMEMC_move")
 GOMC_PROFILE_EVENT(PREP_CRANKSHAFT, "prepare_crankshaft_move")
@@ -46,6 +48,7 @@ GOMC_PROFILE_EVENT(PREP_CFCMC, "prepare_CFCMC_move")
 GOMC_PROFILE_EVENT(TRANS_DISPLACE, "transform_translate_move")
 GOMC_PROFILE_EVENT(TRANS_ROTATE, "transform_rotate_move")
 GOMC_PROFILE_EVENT(TRANS_MULTIPARTICLE, "transform_multiParticle_move")
+GOMC_PROFILE_EVENT(TRANS_MULTIPARTICLE_BM, "transform_multiParticleBM_move")
 GOMC_PROFILE_EVENT(TRANS_INTRA_SWAP, "transform_intraSwap_move")
 GOMC_PROFILE_EVENT(TRANS_INTRA_MEMC, "transform_intraMEMC_move")
 GOMC_PROFILE_EVENT(TRANS_CRANKSHAFT, "transform_crankshaft_move")
@@ -59,6 +62,7 @@ GOMC_PROFILE_EVENT(TRANS_CFCMC, "transform_CFCMC_move")
 GOMC_PROFILE_EVENT(CALC_EN_DISPLACE, "cal_energy_translate_move")
 GOMC_PROFILE_EVENT(CALC_EN_ROTATE, "cal_energy_rotate_move")
 GOMC_PROFILE_EVENT(CALC_EN_MULTIPARTICLE, "cal_energy_multiParticle_move")
+GOMC_PROFILE_EVENT(CALC_EN_MULTIPARTICLE_BM, "cal_energy_multiParticleBM_move")
 GOMC_PROFILE_EVENT(CALC_EN_INTRA_SWAP, "cal_energy_intraSwap_move")
 GOMC_PROFILE_EVENT(CALC_EN_INTRA_MEMC, "cal_energy_intraMEMC_move")
 GOMC_PROFILE_EVENT(CALC_EN_CRANKSHAFT, "cal_energy_crankshaft_move")
@@ -72,6 +76,7 @@ GOMC_PROFILE_EVENT(CALC_EN_CFCMC, "cal_energy_CFCMC_move")
 GOMC_PROFILE_EVENT(ACC_DISPLACE, "accept_translate_move")
 GOMC_PROFILE_EVENT(ACC_ROTATE, "accept_rotate_move")
 GOMC_PROFILE_EVENT(ACC_MULTIPARTICLE, "accept_multiParticle_move")
+GOMC_PROFILE_EVENT(ACC_MULTIPARTICLE_BM, "accept_multiParticleBM_move")
 GOMC_PROFILE_EVENT(ACC_INTRA_SWAP, "accept_intraSwap_move")
 GOMC_PROFILE_EVENT(ACC_INTRA_MEMC, "accept_intraMEMC_move")
 GOMC_PROFILE_EVENT(ACC_CRANKSHAFT, "accept_crankshaft_move")

src/GPU/CalculateMinImageCUDAKernel.cuh

@@ -38,6 +38,47 @@ __device__ inline void TransformUnSlantGPU(double3 & dist,
   dist.z = slant.x * gpu_Invcell_z[0] + slant.y * gpu_Invcell_z[1] + slant.z * gpu_Invcell_z[2];
 }
 
+
+__device__ inline void WrapPBC(double &v, double &ax)
+{
+  if(v >= ax)
+    v -= ax;
+  else if(v < 0)
+    v += ax;
+}
+
+__device__ inline void WrapPBC_f3(double3 &v, double3 &ax)
+{
+  WrapPBC(v.x, ax.x);
+  WrapPBC(v.y, ax.y);
+  WrapPBC(v.z, ax.z);
+}
+
+__device__ inline void  UnwrapPBC(
+  double &v,
+  double &ref, 
+  double &ax,
+  double &halfax)
+{
+  if(abs(ref - v) > halfax) {
+    if(ref < halfax)
+      v -= ax;
+    else
+      v += ax;
+  }
+}
+
+__device__ inline void UnwrapPBC_f3(
+  double3 &v,
+  double3 &ref, 
+  double3 &ax,
+  double3 &halfax)
+{
+  UnwrapPBC(v.x, ref.x, ax.x, halfax.x);
+  UnwrapPBC(v.y, ref.y, ax.y, halfax.y);
+  UnwrapPBC(v.z, ref.z, ax.z, halfax.z);
+}
+
 __device__ inline double MinImageSignedGPU(double raw, double ax, double halfAx)
 {
   if (raw > halfAx)

src/GPU/ConstantDefinitionsCUDAKernel.cu

@@ -373,6 +373,7 @@ void DestroyCUDAVars(VariablesCUDA *vars)
   CUFREE(vars->gpu_cellVector);
   CUFREE(vars->gpu_mapParticleToCell);
   CUFREE(vars->gpu_nonOrth);
+  CUFREE(vars->gpu_startAtomIdx);
   for(uint b = 0; b < BOX_TOTAL; b++) {
     CUFREE(vars->gpu_cell_x[b]);
     CUFREE(vars->gpu_cell_y[b]);