ioSaturn merged with master

CMakeLists.txt

@@ -7,7 +7,7 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
 #Versioning
 set (GOMC_VERSION_MAJOR 1)
-set (GOMC_VERSION_MINOR 00)
+set (GOMC_VERSION_MINOR 17)
 
 IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE Release CACHE STRING
@@ -38,6 +38,7 @@ elseif(MSVC)
     set(CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT "${CMAKE_CXX_FLAGS_RELWITHDEBINFO_INIT} /MT /Zi /O2 /Ob1 /D NDEBUG")
 endif()
 
+
 #EnsemblePreprocessor defines NVT = 1, GEMC = 2, GCMC = 3
 #Grand Canonical Monte Carlo
 set(GC_flags "-DENSEMBLE=3")

Change log

@@ -1,10 +1,41 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [1.6] - 03/24/2016
++ Code cleaning
+
+## [1.5] - 03/24/2016
++ Support for Ewald Summation
+
+## [1.1] - 01/20/2016
++ Supporting Martini forcefield
+
 ## [1.0] - 10/18/2015
 + Changes for input file system.
 + Added Cell list optimization to the GPU and the Serial code.
 
+##[1.00] - 12/4/2015
++ Added Examples of water and DME for NVT and GCMC
++ Added bin/linux, which contains all executable files for linux
+
+##[1.00] Ewald branch - 12/8/2015
++ Improve the initialization of Ewald's parameters, so that non-ewald simulation can also run on ewald code without crashing.
++ CMakeList.txt file is added.
+
+##[1.00] - 12/22/2015
++ Update CPUSide.cpp, move hist into the ifdef of GCMC. Target at the floating operation issue returned by NVT and GEMC simulations.
+
+##[1.00] - 01/25/2016
++ Fix the coherence issue on two boxes simulations, including NPT, GEMC, and two boxes GCMC simulations.
+
++ To fix the issue, Calp() and SetupRecip() have to be recalculated everytime before and after the volume transfer; RecipSinSum and RecipCosSum arrays have to be synchronized in two boxes simulations; GEMC_NVT is different from GEMC_NPT, the difference between GEMC_NVT and GEMC_NPT requires "if" statement.
+
+? GEMC is returning good result from computation; however, it does not return correct results. A potential bug inside of the computation logic.
+
+##[1.00] - -3/15/2016
++ Fix the bug of GEMC simulation. Now all NVT, GCMC, and GEMC are working.
++ Enable the Cache version of GEMC to save time; however, the scalability is limited.
+
 ## [0.972] - 5/11/2015
 + Fixes for PDB output for NVT in the GPU code.
 
@@ -18,4 +49,5 @@ All notable changes to this project will be documented in this file.
 + Fixed calculation of angular weights for branched molecules coupled-decoupled configuration bias algorithm.
 + Improved move adjustments for better targeting of desired acceptance rate.
 + Various minor bug fixes for fringe conditions.
-+ Improvements to I/O handling, inclusion of new output types relating to grand canonical ensemble (fluctuations, energy/particle samples, and distribution of molecule counts).
++ Improvements to I/O handling, inclusion of new output types relating to grand canonical ensemble (fluctuations, energy/particle samples, and distribution of molecule counts).
+

lib/BasicTypes.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef BASIC_TYPES_H
 #define BASIC_TYPES_H
 
@@ -58,4 +51,3 @@ struct XYZ
 };
 
 #endif /*BASIC_TYPES_H*/
-

lib/BitLib.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef BIT_LIB_H
 #define BIT_LIB_H
 
@@ -35,4 +28,3 @@ namespace bits
 }
 
 #endif /*BIT_LIB_H*/
-

lib/GeomLib.h

@@ -1,13 +1,11 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef GEOM_LIB_H
 #define GEOM_LIB_H
 
+//Standard way to get pi constant on most platforms
+//Needs to be defined _before_ including  math.h
+//so that the PI constants come from math.h
+#define _USE_MATH_DEFINES
+
 #include <math.h> //For sqrt, fabs, M_PI
 #include <limits> //for double limits
 
@@ -17,10 +15,7 @@ along with this program, also can be found at <http://www.gnu.org/licenses/>.
 //  DEFINES  //
 ///////////////
 
-//Standard way to get pi constant on most platforms
-#define _USE_MATH_DEFINES
-
-//In case that didn't work
+//Just in case any of these weren't included from math.h
 #ifndef M_PI
 //From Mathematica: 
 //N[Pi, 75]
@@ -104,4 +99,3 @@ namespace geom
 }
 
 #endif /*GEOM_LIB_H*/
-

lib/NumLib.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef NUMERIC_LIB_H
 #define NUMERIC_LIB_H
 
@@ -15,6 +8,8 @@ along with this program, also can be found at <http://www.gnu.org/licenses/>.
 namespace num
 {
    static const double dbl_margin = 0.00001;
+   static const double qqFact = 167000.00;
+   static const double BIGNUM = 10E40;
    static const uint VDW_STD_KIND = 0, VDW_SHIFT_KIND = 1, VDW_SWITCH_KIND = 2;
 
    template <typename T>
@@ -36,16 +31,16 @@ namespace num
       BoundGt<T>(val, upper);
    }
 
-   //Arithmatic mean
+   //Arithmetic mean.
    inline double MeanA(const uint v1, const uint v2) { return (v1+v2)/2.0; }
    //Geometric mean.
    inline double MeanG(const double v1, const double v2) { return sqrt(v1*v2); }
-   //Arithmatic mean
+   //Arithmetic mean.
    inline double MeanA(std::vector<double> const& v1,
 		       std::vector<double> const& v2,
                        const uint ix1, const uint ix2) 
    { return (v1[ix1]+v2[ix2])*0.5; }
-   //Arithmatic mean
+   //Arithmetic mean.
    inline double MeanA(std::vector<uint> const& v1,
                        std::vector<uint> const& v2,
                        const uint ix1, const uint ix2)
@@ -62,9 +57,12 @@ namespace num
                        const uint ix1, const uint ix2)
    { return sqrt(v1[ix1]*v2[ix2]); }
 
-   inline double Sq(const double v) { return v * v; }
-   inline double Cb(const double v) { return v * v * v; }
-   inline void Cb(double & s, double & c, const double v)
+   template <class Type>
+   inline Type Sq(const Type v) { return v * v; }
+   template <class Type>
+   inline Type Cb(const Type v) { return v * v * v; }
+   template <class Type>
+   inline void Cb(Type & s, Type & c, const Type v)
    { s = v * v; c = s * v; }
 
    inline double POW(const double d2, const double d4, const double d6,
@@ -106,4 +104,3 @@ namespace num
 }
 
 #endif /*NUMERIC_LIB_H*/
-

lib/StrLib.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef STR_LIB_H
 #define STR_LIB_H
 
@@ -73,4 +66,3 @@ namespace str
 }
 
 #endif /*STR_LIB_H*/
-

lib/StrStrmLib.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef STR_STRM_LIB_H
 #define STR_STRM_LIB_H
 
@@ -197,4 +190,3 @@ namespace sstrm
 }
 
 #endif /*STR_STRM_LIB_H*/
-

lib/VectorLib.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef VECTOR_LIB_H
 #define VECTOR_LIB_H
 
@@ -75,4 +68,3 @@ namespace vect
 }
 
 #endif /*VECTOR_LIB_H*/
-

src/BlockOutput.cpp

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #include "BlockOutput.h"
 #include "PDBConst.h"
 #include "OutConst.h"
@@ -222,4 +215,3 @@ void BlockAverages::InitWatchMulti(config_setup::TrackedVars const& tracked)
    }
 #endif
 }
-

src/BlockOutput.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef BLOCK_OUTPUT_H
 #define BLOCK_OUTPUT_H
 
@@ -124,4 +117,3 @@ struct BlockAverages : OutputableBase
 };
 
 #endif /*BLOCK_OUTPUT_H*/
-

src/BoxDimensions.cpp

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #include "BoxDimensions.h"
 #include "MoveConst.h" //For cutoff-related fail condition
 
@@ -85,4 +78,3 @@ uint BoxDimensions::ExchangeVolume
    }
    return state;
 }
-

src/BoxDimensions.h

@@ -1,10 +1,3 @@
-/*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 1.0 (Serial version)
-Copyright (C) 2015  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/>.
-********************************************************************************/
 #ifndef BOX_DIMENSIONS_H
 #define BOX_DIMENSIONS_H
 
@@ -24,7 +17,7 @@ along with this program, also can be found at <http://www.gnu.org/licenses/>.
 
 //TODO:
 //Rename to PeriodicBoxes at some point.
-struct BoxDimensions
+class BoxDimensions
 {
  public:
    BoxDimensions() {}
@@ -125,7 +118,7 @@ struct BoxDimensions
    void GetDistSq(double & distSq, XYZArray const& arr, const uint i,
 		  const uint j, const uint b) const;
 
-   
+//private:
    XYZArray axis;     //x, y, z dimensions of each box (a)
    XYZArray halfAx;   //x, y, z dimensions / 2 of each box (a)
    double volume[BOX_TOTAL];     //volume of each box in (a^3)
@@ -143,6 +136,9 @@ struct BoxDimensions
 
    double UnwrapPBC(double& v, const double ref,
 		    const double ax, const double halfAx) const;
+
+   double DotProduct(const uint atom, double kx, double ky,
+		     double kz, const XYZArray & Coords, uint box) const; 
 };
 
 inline BoxDimensions::BoxDimensions(BoxDimensions const& other) : 
@@ -494,5 +490,13 @@ inline double BoxDimensions::UnwrapPBC
 #endif
 }
 
-#endif /*BOX_DIMENSIONS_H*/
+//Calculate dot product
+inline double BoxDimensions::DotProduct(const uint atom, double kx,
+					double ky, double kz,
+					const XYZArray &Coords, uint box) const
+{
+   double x = Coords.x[atom], y = Coords.y[atom], z = Coords.z[atom];
+   return(x * kx + y * ky + z * kz);
+}
 
+#endif /*BOX_DIMENSIONS_H*/