Standardize guards on header files. Add some missing ones.

lib/AlphaNum.h

@@ -5,7 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef ALPHA_NUM_H
+#define ALPHA_NUM_H
+
 #include "BasicTypes.h" // uint
 #include <algorithm>
 #include <cassert>
@@ -40,4 +42,6 @@ class AlphaNum {
   uint string2Uint(std::string stringSuffix);
   struct icompare_char;
   struct compare;
-};
+};
+
+#endif /*ALPHA_NUM_H*/

lib/FloydWarshallCycle.h

@@ -5,7 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef FLOYD_WARSHALL_CYCLE_H
+#define FLOYD_WARSHALL_CYCLE_H
+
 #include <algorithm>
 #include <cassert>
 #include <vector>
@@ -86,3 +88,5 @@ class FloydWarshallCycle {
   std::vector<int> returnCombinedSet(const std::vector<int> &first,
                                      const std::vector<int> &second);
 };
+
+#endif /*FLOYD_WARSHALL_CYCLE_H*/

src/BondAdjacencyList.h

@@ -8,8 +8,8 @@ along with this program, also can be found at
 
 /* Courtesy of https://www.softwaretestinghelp.com/graph-implementation-cpp/ */
 
-#ifndef BONDADJACENCYLIST_H
-#define BONDADJACENCYLIST_H
+#ifndef BOND_ADJACENCY_LIST_H
+#define BOND_ADJACENCY_LIST_H
 
 #include <limits.h>
 
@@ -48,4 +48,4 @@ class BondAdjacencyList {
 
   graphEdge *edges;
 };
-#endif
+#endif /*BOND_ADJACENCY_LIST_H*/

src/CBMC.h

@@ -66,4 +66,4 @@ CBMC *MakeCBMC(System &sys, const Forcefield &ff, const MoleculeKind &kind,
                const Setup &set);
 } // namespace cbmc
 
-#endif
+#endif /*CBMC_H*/

src/CalculateEnergy.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef CALCULATEENERGY_H
-#define CALCULATEENERGY_H
+#ifndef CALCULATE_ENERGY_H
+#define CALCULATE_ENERGY_H
 
 #include <vector>
 
@@ -294,4 +294,4 @@ class CalculateEnergy {
   const CellList &cellList;
 };
 
-#endif /*ENERGY_H*/
+#endif /*CALCULATE_ENERGY_H*/

src/CellList.h

@@ -254,4 +254,4 @@ inline void CellList::Pairs::Next() {
     // skip over doubles
   } while (First() >= Second());
 }
-#endif
+#endif /*CELLLIST_H*/

src/Checkpoint.h

@@ -169,4 +169,4 @@ class Checkpoint {
   }
 };
 
-#endif
+#endif /*CHECKPOINT_H*/

src/CheckpointOutput.h

@@ -65,4 +65,4 @@ class CheckpointOutput : public OutputableBase {
   ulong stepsPerCheckpoint;
 };
 
-#endif
+#endif /*CHECKPOINT_OUTPUT_H*/

src/CheckpointSetup.h

@@ -97,4 +97,4 @@ class CheckpointSetup {
   friend class CheckpointOutput;
 };
 
-#endif
+#endif /*CHECKPOINT_SETUP_H*/

src/ConfigSetup.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef CONFIGSETUP_H
-#define CONFIGSETUP_H
+#ifndef CONFIG_SETUP_H
+#define CONFIG_SETUP_H
 
 #include <iostream> //for cerr, cout;
 #include <map>      //for function handle storage.
@@ -918,4 +918,4 @@ class ConfigSetup {
   InputFileReader reader;
 };
 
-#endif
+#endif /*CONFIG_SETUP_H*/

src/CoordinateSetup.h

@@ -21,4 +21,4 @@ struct CoordinateSetup {
   void SetCOM(const MolSetupData &molData);
 }
 
-#endif
+#endif /*COORDINATESETUP_H*/

src/DCDlib.h

@@ -112,4 +112,4 @@ void NAMD_bug(const char *err_msg);
 int NAMD_file_exists(const char *filename);
 void NAMD_backup_file(const char *filename, const char *extension);
 
-#endif /* ! DCDLIB_H */
+#endif /*DCDLIB_H*/

src/EnergyTypes.h

@@ -539,4 +539,4 @@ inline std::ostream &operator<<(std::ostream &out, Energy &en) {
 }
 #endif
 
-#endif
+#endif /*ENERGYTYPES_H*/

src/EwaldCached.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef EWALDCACHED_H
-#define EWALDCACHED_H
+#ifndef EWALD_CACHED_H
+#define EWALD_CACHED_H
 
 #include "Ewald.h"
 
@@ -81,4 +81,4 @@ class EwaldCached : public Ewald {
 #endif
 };
 
-#endif /*EWALDCACHED_H*/
+#endif /*EWALD_CACHED_H*/

src/ExtendedSystem.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef EXTENDED_SYSTEM
-#define EXTENDED_SYSTEM
+#ifndef EXTENDED_SYSTEM_H
+#define EXTENDED_SYSTEM_H
 
 #include <vector>
 
@@ -83,4 +83,4 @@ class ExtendedSystem {
   std::vector<XYZ> binaryVeloc;
 };
 
-#endif /*EXTENDED_SYSTEM*/
+#endif /*EXTENDED_SYSTEM_H*/

src/ExtendedSystemOutput.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef DCD_OUTPUT_H
-#define DCD_OUTPUT_H
+#ifndef EXTENDED_SYSTEM_OUTPUT_H
+#define EXTENDED_SYSTEM_OUTPUT_H
 
 #include <cstring>
 #include <iostream>
@@ -124,4 +124,4 @@ struct ExtendedSystemOutput : OutputableBase {
   Writer xscFile[BOX_TOTAL];
 };
 
-#endif /*DCD_OUTPUT_H*/
+#endif /*EXTENDED_SYSTEM_OUTPUT_H*/

src/FreeEnergyOutput.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef FREEENERGY_OUTPUT_H
-#define FREEENERGY_OUTPUT_H
+#ifndef FREE_ENERGY_OUTPUT_H
+#define FREE_ENERGY_OUTPUT_H
 
 #include <fstream>
 #include <string>
@@ -59,4 +59,4 @@ struct FreeEnergyOutput : OutputableBase {
 #endif
 };
 
-#endif /*HIST_OUTPUT_H*/
+#endif /*FREE_ENERGY_OUTPUT_H*/

src/FxdWidthWrtr.h

@@ -5,8 +5,8 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef FXD_WIDTH_WRTR
-#define FXD_WIDTH_WRTR
+#ifndef FXD_WIDTH_WRTR_H
+#define FXD_WIDTH_WRTR_H
 
 struct FxdWidthWrtr : Writer {
   FxdWidthWrtr(std::string const &nm, std::string const &als, const bool crit,
@@ -23,4 +23,4 @@ struct FxdWidthWrtr : Writer {
   // Align left by default, but accept right alignment if necessary.
 }
 
-#endif /*FXD_WIDTH_WRTR*/
+#endif /*FXD_WIDTH_WRTR_H*/

src/GOMCEventsProfileDef.h

@@ -5,6 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
+#ifndef GOMC_EVENTS_PROFILE_DEF_H
+#define GOMC_EVENTS_PROFILE_DEF_H
+
 GOMC_PROFILE_EVENT(INITIALIZE, "initialization")
 GOMC_PROFILE_EVENT(MC_RUN, "MC_run")
 GOMC_PROFILE_EVENT(DESTRUCTION, "destruction")
@@ -152,3 +155,5 @@ GOMC_PROFILE_EVENT(DUMMY_EVENT19, "Dummy Event19")
 GOMC_PROFILE_EVENT(DUMMY_EVENT20, "Dummy Event20")
 GOMC_PROFILE_EVENT(DUMMY_EVENT21, "Dummy Event21")
 GOMC_PROFILE_EVENT(DUMMY_EVENT22, "Dummy Event22")
+
+#endif /*GOMC_EVENTS_PROFILE_DEF_H*/

src/GPU/CUDAMemoryManager.cuh

@@ -4,7 +4,9 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef CUDA_MEMORY_MANAGER_H
+#define CUDA_MEMORY_MANAGER_H
+
 #ifdef GOMC_CUDA
 #include <cuda.h>
 #include <cuda_runtime.h>
@@ -27,3 +29,4 @@ private:
 };
 
 #endif
+#endif /*CUDA_MEMORY_MANAGER_H*/

src/GPU/CalculateEnergyCUDAKernel.cuh

@@ -4,7 +4,9 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef CALCULATE_ENERGY_CUDA_KERNEL_H
+#define CALCULATE_ENERGY_CUDA_KERNEL_H
+
 #ifdef GOMC_CUDA
 #include <cuda.h>
 #include <cuda_runtime.h>
@@ -206,3 +208,4 @@ __device__ double CalcEnSwitchGPUNoLambda(double distSq, int index,
     double gpu_rCut, double gpu_rOn);
 
 #endif /*GOMC_CUDA*/
+#endif /*CALCULATE_ENERGY_CUDA_KERNEL_H*/

src/GPU/CalculateEwaldCUDAKernel.cuh

@@ -4,8 +4,8 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef CALCULATE_EWALD_CUDA_KERNEL
-#define CALCULATE_EWALD_CUDA_KERNEL
+#ifndef CALCULATE_EWALD_CUDA_KERNEL_H
+#define CALCULATE_EWALD_CUDA_KERNEL_H
 
 #ifdef GOMC_CUDA
 #include <cuda.h>
@@ -190,4 +190,4 @@ __global__ void BoxReciprocalGPU(double *gpu_prefact,
                                  int imageSize);
 
 #endif /*GOMC_CUDA*/
-#endif /*CALCULATE_EWALD_CUDA_KERNEL*/
+#endif /*CALCULATE_EWALD_CUDA_KERNEL_H*/

src/GPU/CalculateForceCUDAKernel.cuh

@@ -4,8 +4,8 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef CALCULATE_FORCE_CUDA_KERNEL
-#define CALCULATE_FORCE_CUDA_KERNEL
+#ifndef CALCULATE_FORCE_CUDA_KERNEL_H
+#define CALCULATE_FORCE_CUDA_KERNEL_H
 
 #ifdef GOMC_CUDA
 #include <vector>
@@ -403,4 +403,4 @@ __device__ inline double CalcCoulombForceGPU(double distSq, double qi_qj,
 
 
 #endif /*GOMC_CUDA*/
-#endif /*CALCULATE_FORCE_CUDA_KERNEL*/
+#endif /*CALCULATE_FORCE_CUDA_KERNEL_H*/

src/GPU/CalculateMinImageCUDAKernel.cuh

@@ -5,7 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef CALCULATE_MIN_IMAGE_CUDA_KERNEL_H
+#define CALCULATE_MIN_IMAGE_CUDA_KERNEL_H
+
 #ifdef GOMC_CUDA
 
 #include "ConstantDefinitionsCUDAKernel.cuh"
@@ -278,3 +280,4 @@ static __inline__ __device__ double atomicAdd(double *address, double val) {
 #endif
 
 #endif /*GOMC_CUDA*/
+#endif /*CALCULATE_MIN_IMAGE_CUDA_KERNEL_H*/

src/GPU/ConstantDefinitionsCUDAKernel.cuh

@@ -4,8 +4,8 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#ifndef CONSTANT_DEFINITIONS_CUDA_KERNEL
-#define CONSTANT_DEFINITIONS_CUDA_KERNEL
+#ifndef CONSTANT_DEFINITIONS_CUDA_KERNEL_H
+#define CONSTANT_DEFINITIONS_CUDA_KERNEL_H
 
 #ifdef GOMC_CUDA
 #include <cuda.h>
@@ -47,4 +47,4 @@ void DestroyExp6CUDAVars(VariablesCUDA *vars);
 void DestroyCUDAVars(VariablesCUDA *vars);
 
 #endif /*GOMC_CUDA*/
-#endif /*CONSTANT_DEFINITIONS_CUDA_KERNEL*/
+#endif /*CONSTANT_DEFINITIONS_CUDA_KERNEL_H*/

src/GPU/TransformParticlesCUDAKernel.cuh

@@ -5,7 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef TRANSFORM_PARTICLES_CUDA_KERNEL_H
+#define TRANSFORM_PARTICLES_CUDA_KERNEL_H
+
 #ifdef GOMC_CUDA
 #include "Random123/philox.h"
 #include <vector>
@@ -95,3 +97,4 @@ __global__ void BrownianMotionTranslateKernel(
     unsigned int key, ulong seed, double BETA);
 
 #endif
+#endif /*TRANSFORM_PARTICLES_CUDA_KERNEL_H*/

src/GPU/VariablesCUDA.cuh

@@ -4,9 +4,10 @@ Copyright (C) 2022 GOMC Group
 A copy of the MIT License can be found in License.txt
 along with this program, also can be found at <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
-#ifdef GOMC_CUDA
+#ifndef VARIABLES_CUDA_H
+#define VARIABLES_CUDA_H
 
+#ifdef GOMC_CUDA
 #include <cuda.h>
 #include <stdio.h>
 #include <cuda_runtime.h>
@@ -135,3 +136,4 @@ public:
   int *gpu_cellVector, *gpu_mapParticleToCell;
 };
 #endif
+#endif /*VARIABLES_CUDA_H*/

src/Geometry.h

@@ -138,4 +138,4 @@ class SortedNonbond {
   SubdividedArray subdiv;
 };
 
-#endif
+#endif /*GEOMETRY_H*/

src/InputFileReader.h

@@ -5,7 +5,9 @@ A copy of the MIT License can be found in License.txt
 along with this program, also can be found at
 <https://opensource.org/licenses/MIT>.
 ********************************************************************************/
-#pragma once
+#ifndef INPUT_FILE_READER_H
+#define INPUT_FILE_READER_H
+
 #include <fstream>
 #include <iostream>
 #include <vector>
@@ -23,3 +25,5 @@ class InputFileReader {
   InputFileReader(void);
   ~InputFileReader();
 };
+
+#endif /*INPUT_FILE_READER_H*/