Merge pull request #55 from GOMC-WSU/development

Version 2.1

CMakeLists.txt

@@ -11,7 +11,7 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 #Versioning
 set (GOMC_VERSION_MAJOR 2)
-set (GOMC_VERSION_MINOR 00)
+set (GOMC_VERSION_MINOR 10)
 
 IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE Release CACHE STRING
@@ -35,9 +35,14 @@ configure_file(
 	)
 include_directories("${PROJECT_BINARY_DIR}")
 
-if(CMAKE_COMPILER_IS_CNUCXX)
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -stdlib=libstdc++") 
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -stdlib=libstdc++")
+endif()
+
+if(CMAKE_COMPILER_IS_GNUCXX)
     set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall") 
-    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -Wall") 
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
 elseif(MSVC)
     set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} /D_DEBUG /MTd /Zi /Ob0 /Od /RTC1")
     set(CMAKE_CXX_FLAGS_DEBUG_INIT "${CMAKE_CXX_FLAGS_DEBUG_INIT} /D_DEBUG /MTd /Zi /Ob0 /Od /RTC1")

Change log

@@ -1,6 +1,15 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.1] - 9/4/2017
++ Adsorption
++ Fixed the bug where GPU and CPU total energy calculations where slighty different.
++ Removed some unused variables
++ Removed some warnings
++ Fixed pow function ambiguity in some compilers like clang
++ Fixed compiling bug for Clock.h when using clang (mac users)
++ Set a maximum of 9999999999 for output energies
+
 ## [2.0] - 6/11/2017
 + NPT added
 + GPU implementation has been added to the project

README.md

@@ -1,4 +1,4 @@
-Current Release: 2.0 (6/11/2017)
+Current Release: 2.1 (9/4/2017)
 
 [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/GOMC_WSU/Lobby?utm_source=share-link&utm_medium=link&utm_campaign=share-link)
 

lib/BasicTypes.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/BitLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/GeomLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/NumLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/StrLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/StrStrmLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

lib/VectorLib.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

metamake.sh

@@ -3,3 +3,4 @@
 mkdir -p bin
 cd bin
 cmake ..
+make

src/BlockOutput.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -54,15 +54,24 @@ void BlockAverage::Sum(void)
       block[b] += *dblSrc[b] * scl;
 }
 
-void BlockAverage::DoWrite(const ulong step)
+void BlockAverage::DoWrite(const ulong step, uint precision)
 {
   if (tot >= 1)
   {
     if (outBlock0->is_open())
     {
-      (*outBlock0) << left << std::fixed  << std::setprecision(4) <<
-	std::setw(OUTPUTWIDTH);
-      (*outBlock0) << block[0];
+      if(abs(block[0]) > 9999999999.9999)
+      {
+	(*outBlock0) << left << std::fixed  << std::setprecision(0) <<
+	  std::setw(OUTPUTWIDTH);
+	(*outBlock0) << 9999999999;
+      }
+      else
+      {
+	(*outBlock0) << left << std::fixed  << std::setprecision(precision) <<
+	  std::setw(OUTPUTWIDTH);
+	(*outBlock0) << block[0];
+      }
     }
     else
       std::cerr << "Unable to write to Box_0 output file" << std::endl;
@@ -71,9 +80,18 @@ void BlockAverage::DoWrite(const ulong step)
   {
     if (outBlock1->is_open())
     {
-      (*outBlock1) << left << std::fixed  << std::setprecision(4) <<
-	std::setw(OUTPUTWIDTH);
-      (*outBlock1) << block[1];
+      if(abs(block[0]) > 9999999999.9999)
+      {
+	(*outBlock1) << left << std::fixed  << std::setprecision(0) <<
+	  std::setw(OUTPUTWIDTH);
+	(*outBlock1) << 9999999999;
+      }
+      else
+      {
+	(*outBlock1) << left << std::fixed  << std::setprecision(precision) <<
+	  std::setw(OUTPUTWIDTH);
+	(*outBlock1) << block[1];
+      }
     }
     else
       std::cerr << "Unable to write to Box_1 output file" << std::endl;
@@ -124,17 +142,22 @@ void BlockAverages::DoOutput(const ulong step)
   outBlock0 << left << std::fixed << std::setw(OUTPUTWIDTH) << nextStep;
   outBlock1 << left << std::fixed << std::setw(OUTPUTWIDTH) << nextStep;
   for (uint v = 0; v < totalBlocks; ++v)
-    blocks[v].Write(nextStep, firstPrint);
+  {
+    if(v < out::TOTAL_SINGLE)
+      blocks[v].Write(nextStep, firstPrint);
+    else
+      blocks[v].Write(nextStep, firstPrint, 8);
+  }
   outBlock0 << std::endl;
   if(outBlock1.is_open())
     outBlock1 << std::endl;
 }
 
 void BlockAverages::InitWatchSingle(config_setup::TrackedVars const& tracked)
 {
-  outBlock0 << left << std::fixed << std::setw(OUTPUTWIDTH) << "STEPS";
+  outBlock0 << left << std::fixed << std::setw(OUTPUTWIDTH) << "#STEPS";
   if(outBlock1.is_open())
-    outBlock1 << left << std::fixed << std::setw(OUTPUTWIDTH) << "STEPS";
+    outBlock1 << left << std::fixed << std::setw(OUTPUTWIDTH) << "#STEPS";
   //Note: The order of Init should be same as order of SetRef
   blocks[out::ENERGY_TOTAL_IDX].Init(&outBlock0, &outBlock1, tracked.energy.block, invSteps, out::ENERGY_TOTAL, BOXES_WITH_U_NB);
   blocks[out::ENERGY_INTER_IDX].Init(&outBlock0, &outBlock1, tracked.energy.block, invSteps, out::ENERGY_INTER, BOXES_WITH_U_NB);
@@ -217,13 +240,25 @@ void BlockAverages::InitWatchMulti(config_setup::TrackedVars const& tracked)
 void BlockAverage::printTitle(std::string output, uint boxes)
 {
   if(tot>=1)
+  {
     if((*outBlock0).is_open())
+    {
       (*outBlock0) << left << std::fixed << std::setw(OUTPUTWIDTH) << output;
+    }
     else
+    {
       std::cerr << "Unable to write to Block_0 output file!" << std::endl;
+    }
+  }
   if(tot>=2)
+  {
     if((*outBlock1).is_open())
+    {
       (*outBlock1) << left << std::fixed << std::setw(OUTPUTWIDTH) << output;
+    }
     else
+    {
       std::cerr << "Unable to write to Block_1 output file!" << std::endl;
+    }
+  }
 }

src/BlockOutput.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.
@@ -63,11 +63,11 @@ struct BlockAverage
     dblSrc[b] = NULL;
   }
   void Sum(void);
-  void Write(const ulong step, const bool firstPrint)
+  void Write(const ulong step, const bool firstPrint, uint precision = 4)
   {
     first = firstPrint;
     if (enable)
-      DoWrite(step);
+      DoWrite(step, precision);
   }
 
 private:
@@ -77,7 +77,7 @@ struct BlockAverage
       block[b] = 0.0;
     samples = 0;
   }
-  void DoWrite(const ulong step);
+  void DoWrite(const ulong step, uint precision);
   void printTitle(std::string output, uint boxes);
 
   std::ofstream* outBlock0;
@@ -93,9 +93,12 @@ struct BlockAverage
 /**********************************************************************/
 struct BlockAverages : OutputableBase
 {
+  BlockAverages(): blocks(NULL) {}
+
   BlockAverages(OutputVars & v)
   {
     this->var = &v;
+    blocks = NULL;
   }
 
   ~BlockAverages(void)
@@ -108,7 +111,10 @@ struct BlockAverages : OutputableBase
     {
       outBlock1.close();
     }
-    if ( blocks != NULL ) delete[] blocks;
+    if ( blocks != NULL )
+    {
+      delete[] blocks;
+    }
   }
   //No additional init.
   virtual void Init(pdb_setup::Atoms const& atoms,

src/BoxDimensions.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/BoxDimensions.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CBMC.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CBMC.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/COM.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CPUSide.cpp

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.

src/CPUSide.h

@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.0
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.1
 Copyright (C) 2016  GOMC Group
 A copy of the GNU General Public License can be found in the COPYRIGHT.txt
 along with this program, also can be found at <http://www.gnu.org/licenses/>.