fixed header and indentation

HamiedAsadi · Jan 20, 2020 · e6915cf · e6915cf
1 parent 1fc5772
commit e6915cf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,18 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.50] - 1/20/2020
++ Added support for Exponential-6 forcefield
++ Support for multiple simulation with different temperatures
++ Added support for free energy calculations using TI and FEP methods
++ Support for restarting simulation using checkpoint 
++ Added support for new GPU architectures 7.0 and 7.5
++ Added an error message when GPU version was used but there was no GPU present (#126)
++ Read PDB file more efficiently when recalculating trajectory (#131)
++ Fixed detecting simulation box shape (orthogonal and non-orthogonal) (#134)
++ Fixed bugs in PDB reader and support for HETATM field in PDB file
++ Fixed bugs in PSF reader
+
 ## [2.40] - 3/15/2019
 + Added support for Cyclic molecules.
 + Added Inter Molecular Exchange Monte Carlo move in GCMC and GEMC simulation.

diff --git a/CMake/TestMPI.cpp b/CMake/TestMPI.cpp
@@ -1,6 +1,6 @@
-#include <mpi.h> 
+#include <mpi.h>
 
 int main(int argc, char **argv)
 {
-  MPI_Init(&argc,&argv);
+  MPI_Init(&argc, &argv);
 }
diff --git a/CMake/TestWinProcNum.cpp b/CMake/TestWinProcNum.cpp
@@ -2,6 +2,6 @@
 #include <windows.h>
 int main()
 {
-    PROCESSOR_NUMBER p;
-    return 0;
+  PROCESSOR_NUMBER p;
+  return 0;
 }
diff --git a/lib/BasicTypes.h b/lib/BasicTypes.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.40
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.50
 Copyright (C) 2018  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/>.

diff --git a/lib/BitLib.h b/lib/BitLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.40
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.50
 Copyright (C) 2018  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/>.

diff --git a/lib/GeomLib.h b/lib/GeomLib.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.40
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.50
 Copyright (C) 2018  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/>.

diff --git a/lib/Lambda.h b/lib/Lambda.h
@@ -1,5 +1,5 @@
 /*******************************************************************************
-GPU OPTIMIZED MONTE CARLO (GOMC) 2.40
+GPU OPTIMIZED MONTE CARLO (GOMC) 2.50
 Copyright (C) 2018  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/>.
@@ -13,7 +13,8 @@ along with this program, also can be found at <http://www.gnu.org/licenses/>.
 class Lambda
 {
 public:
-  Lambda() {
+  Lambda()
+  {
     std::fill_n(isFraction, BOX_TOTAL, false);
     std::fill_n(lambdaVDW, BOX_TOTAL, 1.0);
     std::fill_n(lambdaCoulomb, BOX_TOTAL, 1.0);
@@ -28,7 +29,7 @@ class Lambda
 
   double GetLambdaVDW(const uint kind, const uint box) const;
 
-  double GetLambdaCoulomb(const uint mol,const uint kind, const uint box) const;
+  double GetLambdaCoulomb(const uint mol, const uint kind, const uint box) const;
 
   double GetLambdaCoulomb(const uint kind, const uint box) const;
 
@@ -47,97 +48,97 @@ class Lambda
 };
 
 inline void Lambda::Set(const double vdw, const double coulomb, const uint mol,
-                const uint kind, const uint box)
+                        const uint kind, const uint box)
 {
-    molIndex[box] = mol;
-    kindIndex[box] = kind;
-    lambdaVDW[box] = vdw;
-    lambdaCoulomb[box] = coulomb;
-    isFraction[box] = true;
+  molIndex[box] = mol;
+  kindIndex[box] = kind;
+  lambdaVDW[box] = vdw;
+  lambdaCoulomb[box] = coulomb;
+  isFraction[box] = true;
 }
 
 inline void Lambda::UnSet(const uint sourceBox, const uint destBox)
 {
-    isFraction[sourceBox] = isFraction[destBox] = false;
-    lambdaVDW[sourceBox] = lambdaCoulomb[sourceBox] = 1.0;
-    lambdaVDW[destBox] = lambdaCoulomb[destBox] = 0.0;
+  isFraction[sourceBox] = isFraction[destBox] = false;
+  lambdaVDW[sourceBox] = lambdaCoulomb[sourceBox] = 1.0;
+  lambdaVDW[destBox] = lambdaCoulomb[destBox] = 0.0;
 }
 
 inline double Lambda::GetLambdaVDW(const uint mol, const uint kind,
-                            const uint box) const
+                                   const uint box) const
 {
-    double val = 1.0;
-    if(isFraction[box]) {
-        if((molIndex[box] == mol) && (kindIndex[box] == kind)) {
-            val = lambdaVDW[box];
-        }
+  double val = 1.0;
+  if(isFraction[box]) {
+    if((molIndex[box] == mol) && (kindIndex[box] == kind)) {
+      val = lambdaVDW[box];
     }
-    return val;
+  }
+  return val;
 }
 
 inline double Lambda::GetLambdaVDW(const uint kind, const uint box) const
 {
-    double val = 1.0;
-    if(isFraction[box]) {
-        if(kindIndex[box] == kind) {
-            val = lambdaVDW[box];
-        }
+  double val = 1.0;
+  if(isFraction[box]) {
+    if(kindIndex[box] == kind) {
+      val = lambdaVDW[box];
     }
-    return val;
+  }
+  return val;
 }
 
 inline double Lambda::GetLambdaCoulomb(const uint mol, const uint kind,
-                                const uint box) const
+                                       const uint box) const
 {
-    double val = 1.0;
-    if(isFraction[box]) {
-        if((molIndex[box] == mol) && (kindIndex[box] == kind)) {
-            val = lambdaCoulomb[box];
-        }
+  double val = 1.0;
+  if(isFraction[box]) {
+    if((molIndex[box] == mol) && (kindIndex[box] == kind)) {
+      val = lambdaCoulomb[box];
     }
-    return val;
+  }
+  return val;
 }
 
 inline double Lambda::GetLambdaCoulomb(const uint kind, const uint box) const
 {
-    double val = 1.0;
-    if(isFraction[box]) {
-        if(kindIndex[box] == kind) {
-            val = lambdaCoulomb[box];
-        }
+  double val = 1.0;
+  if(isFraction[box]) {
+    if(kindIndex[box] == kind) {
+      val = lambdaCoulomb[box];
     }
-    return val;
+  }
+  return val;
 }
 
-inline bool Lambda::KindIsFractional(const uint kind, const uint box) const 
+inline bool Lambda::KindIsFractional(const uint kind, const uint box) const
 {
-    bool result = false;
-    if(isFraction[box]) {
-        if(kindIndex[box] == kind) {
-            result = true;
-        }
+  bool result = false;
+  if(isFraction[box]) {
+    if(kindIndex[box] == kind) {
+      result = true;
     }
-    return result;
+  }
+  return result;
 }
 
 inline uint Lambda::GetKind(const uint box) const
 {
-    if(isFraction[box]) {
-        return kindIndex[box];
-    } else {
-        std::cout << "Error: Lambda.h, calling GetKind\n";
-        exit(EXIT_FAILURE);
-    }
+  if(isFraction[box]) {
+    return kindIndex[box];
+  } else {
+    std::cout << "Error: Lambda.h, calling GetKind\n";
+    exit(EXIT_FAILURE);
+  }
 }
 
 inline uint Lambda::GetMolIndex(const uint box) const
 {
-    if(isFraction[box]) {
-        return molIndex[box];
-    } else {
-        std::cout << "Error: Lambda.h, calling GetKind\n";
-        exit(EXIT_FAILURE);
-    }
+  if(isFraction[box]) {
+    return molIndex[box];
+  } else {
+    std::cout << "Error: Lambda.h, calling GetKind\n";
+    exit(EXIT_FAILURE);
+  }
 }
 
 #endif