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Commit accc4ccd authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods to quiet gcc (Ubuntu 4.3.3-5ubuntu4)

parent 545a83ee
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Showing with 89 additions and 67 deletions
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ accc4ccd
...@@ -504,7 +504,7 @@ void gpuSetAmoebaAngleParameters(amoebaGpuContext amoebaGpu, const std::vector<i ...@@ -504,7 +504,7 @@ void gpuSetAmoebaAngleParameters(amoebaGpuContext amoebaGpu, const std::vector<i
#define DUMP_PARAMETERS 5 #define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 ) #if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > bond_angles - (DUMP_PARAMETERS + 1)) && amoebaGpu->log ) if( (i < DUMP_PARAMETERS || i > bond_angles - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "Angles: %5d [%5d %5d %5d] [%5d %5d %5d] A=%15.7e k[%15.7e %15.7e] [%5d %5d %5d]\n", i, fprintf( amoebaGpu->log, "Angles: %5d [%5d %5d %5d %5d] [%5d %5d] A=%15.7e k=%15.7e [%5d %5d %5d]\n", i,
(*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w, (*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w,
(*psAngleID2)[i].x, (*psAngleID2)[i].y, (*psAngleID2)[i].x, (*psAngleID2)[i].y,
(*psAngleParameter)[i].x, (*psAngleParameter)[i].y, (*psAngleParameter)[i].x, (*psAngleParameter)[i].y,
...@@ -564,7 +564,7 @@ void gpuSetAmoebaInPlaneAngleParameters(amoebaGpuContext amoebaGpu, const std::v ...@@ -564,7 +564,7 @@ void gpuSetAmoebaInPlaneAngleParameters(amoebaGpuContext amoebaGpu, const std::v
#define DUMP_PARAMETERS 5 #define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 ) #if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > bond_angles - (DUMP_PARAMETERS + 1)) && amoebaGpu->log ) if( (i < DUMP_PARAMETERS || i > bond_angles - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "InPlaneAngles: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] A=%15.7e k[%15.7e %15.7e %15.7e %15.7e %15.7e] [%5d %5d %5d %5d]\n", i, fprintf( amoebaGpu->log, "InPlaneAngles: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] A=%15.7e k=%15.7e [%5d %5d %5d %5d]\n", i,
(*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w, (*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w,
(*psAngleID2)[i].x, (*psAngleID2)[i].y, (*psAngleID2)[i].z, (*psAngleID2)[i].w, (*psAngleID2)[i].x, (*psAngleID2)[i].y, (*psAngleID2)[i].z, (*psAngleID2)[i].w,
(*psAngleParameter)[i].x, (*psAngleParameter)[i].y, (*psAngleParameter)[i].x, (*psAngleParameter)[i].y,
...@@ -2100,7 +2100,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu, ...@@ -2100,7 +2100,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
psVdwReductionID->_pSysStream[0][count].w = ii; psVdwReductionID->_pSysStream[0][count].w = ii;
} }
if( ivMapping[ii].size() > 3 ){ if( ivMapping[ii].size() > 3 ){
(void) fprintf( stderr, "Atom %u has %u reductions -- invalid -- aborting", ii, ivMapping[ii].size() ); (void) fprintf( stderr, "Atom %u has %u reductions -- invalid -- aborting", ii, static_cast<unsigned int>(ivMapping[ii].size()) );
exit(1); exit(1);
} }
count++; count++;
...@@ -2335,7 +2335,7 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec ...@@ -2335,7 +2335,7 @@ void amoebaGpuBuildVdwExclusionList( amoebaGpuContext amoebaGpu, const std::vec
for (unsigned int ii = 0; ii < actualAtoms; ii++){ for (unsigned int ii = 0; ii < actualAtoms; ii++){
bool error = false; bool error = false;
if( exclusions[ii].size() != echoExclusions[ii].size() ){ if( exclusions[ii].size() != echoExclusions[ii].size() ){
(void) fprintf( amoebaGpu->log, "\nAtom %6d sz %6u %6u XX\n", ii, exclusions[ii].size(), echoExclusions[ii].size() ); (void) fprintf( amoebaGpu->log, "\nAtom %6d sz %6u %6u XX\n", ii, static_cast<unsigned int>(exclusions[ii].size()), static_cast<unsigned int>(echoExclusions[ii].size()) );
error = true; error = true;
totalErrors++; totalErrors++;
} }
...@@ -2736,7 +2736,7 @@ static int matchMaps( std::string idString, MapIntFloat* map1, MapIntFloat* map ...@@ -2736,7 +2736,7 @@ static int matchMaps( std::string idString, MapIntFloat* map1, MapIntFloat* map
int equalSizes = 1; int equalSizes = 1;
int error = 0; int error = 0;
if( map1->size() != map2->size() ){ if( map1->size() != map2->size() ){
(void) fprintf( log, "%s sizes unequal: %u %u\n", idString.c_str(), map1->size(), map2->size() ); (void) fprintf( log, "%s sizes unequal: %u %u\n", idString.c_str(), static_cast<unsigned int>(map1->size()), static_cast<unsigned int>(map2->size()) );
equalSizes = 0; equalSizes = 0;
error++; error++;
} }
...@@ -3713,7 +3713,7 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId ...@@ -3713,7 +3713,7 @@ void cudaWriteVectorOfDoubleVectorsToFile( char* fname, std::vector<int>& fileId
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
FILE* filePtr = getWriteToFilePtrV( fname, fileId ); FILE* filePtr = getWriteToFilePtrV( fname, fileId );
(void) fprintf( filePtr, "%u\n", outputVector.size() ); (void) fprintf( filePtr, "%u\n", static_cast<unsigned int>(outputVector.size()) );
float values[50]; float values[50];
for ( unsigned int ii = 0; ii < outputVector.size(); ii++ ){ for ( unsigned int ii = 0; ii < outputVector.size(); ii++ ){
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaElectrostatic.cu
View file @ accc4ccd
...@@ -829,7 +829,7 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu ) ...@@ -829,7 +829,7 @@ void cudaComputeAmoebaElectrostatic( amoebaGpuContext amoebaGpu )
if (gpu->bOutputBufferPerWarp){ if (gpu->bOutputBufferPerWarp){
(void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaElectrostaticN2Forces warp: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%u shrd=%u Ebuf=%u ixnCt=%u workUnits=%u\n", (void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaElectrostaticN2Forces warp: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%lu shrd=%lu Ebuf=%u ixnCt=%lu workUnits=%u\n",
amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp, amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp,
sizeof(ElectrostaticParticle), sizeof(ElectrostaticParticle)*threadsPerBlock, amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits ); sizeof(ElectrostaticParticle), sizeof(ElectrostaticParticle)*threadsPerBlock, amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits );
(void) fflush( amoebaGpu->log ); (void) fflush( amoebaGpu->log );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwood.cu
View file @ accc4ccd
...@@ -1971,7 +1971,7 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu ) ...@@ -1971,7 +1971,7 @@ void kCalculateAmoebaKirkwood( amoebaGpuContext amoebaGpu )
if( amoebaGpu->log ){ if( amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaKirkwood: blcks=%u tds=%u %u bPrWrp=%u atm=%u shrd=%u Ebuf=%u ixnCt=%u workUnits=%u\n", (void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaKirkwood: blcks=%u tds=%u %u bPrWrp=%u atm=%lu shrd=%lu Ebuf=%u ixnCt=%lu workUnits=%u\n",
amoebaGpu->nonbondBlocks, threadsPerBlock, maxThreads, amoebaGpu->bOutputBufferPerWarp, amoebaGpu->nonbondBlocks, threadsPerBlock, maxThreads, amoebaGpu->bOutputBufferPerWarp,
sizeof(KirkwoodParticle), sizeof(KirkwoodParticle)*threadsPerBlock, sizeof(KirkwoodParticle), sizeof(KirkwoodParticle)*threadsPerBlock,
amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits ); amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaKirkwoodEDiff.cu
View file @ accc4ccd
...@@ -1031,6 +1031,7 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI, ...@@ -1031,6 +1031,7 @@ __device__ void calculateKirkwoodEDiffPairIxn_kernel( float4 atomCoordinatesI,
} }
#ifdef AMOEBA_DEBUG
__device__ static int debugAccumulate( unsigned int index, float4* debugArray, float* field, unsigned int addMask, float idLabel ) __device__ static int debugAccumulate( unsigned int index, float4* debugArray, float* field, unsigned int addMask, float idLabel )
{ {
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
...@@ -1041,6 +1042,7 @@ __device__ static int debugAccumulate( unsigned int index, float4* debugArray, f ...@@ -1041,6 +1042,7 @@ __device__ static int debugAccumulate( unsigned int index, float4* debugArray, f
return index; return index;
} }
#endif
__device__ void zeroKirkwoodEDiffParticleSharedField( struct KirkwoodEDiffParticle* sA ) __device__ void zeroKirkwoodEDiffParticleSharedField( struct KirkwoodEDiffParticle* sA )
{ {
...@@ -1154,11 +1156,11 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu ) ...@@ -1154,11 +1156,11 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const char* methodName = "kCalculateAmoebaKirkwoodEDiff";
static unsigned int threadsPerBlock = 0; static unsigned int threadsPerBlock = 0;
static int timestep = 0; static int timestep = 0;
timestep++; timestep++;
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
static const char* methodName = "kCalculateAmoebaKirkwoodEDiff";
std::vector<int> fileId; std::vector<int> fileId;
fileId.resize( 2 ); fileId.resize( 2 );
fileId[0] = timestep; fileId[0] = timestep;
...@@ -1201,7 +1203,7 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu ) ...@@ -1201,7 +1203,7 @@ void kCalculateAmoebaKirkwoodEDiff( amoebaGpuContext amoebaGpu )
} }
if( amoebaGpu->log && timestep == 1 ){ if( amoebaGpu->log && timestep == 1 ){
(void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaKirkwoodEDiffN2Forces: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%u shrd=%u Ebuf=%u ixnCt=%u workUnits=%u\n", (void) fprintf( amoebaGpu->log, "kCalculateAmoebaCudaKirkwoodEDiffN2Forces: numBlocks=%u numThreads=%u bufferPerWarp=%u atm=%lu shrd=%lu Ebuf=%u ixnCt=%lu workUnits=%u\n",
amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp, amoebaGpu->nonbondBlocks, threadsPerBlock, amoebaGpu->bOutputBufferPerWarp,
sizeof(KirkwoodEDiffParticle), sizeof(KirkwoodEDiffParticle)*threadsPerBlock, sizeof(KirkwoodEDiffParticle), sizeof(KirkwoodEDiffParticle)*threadsPerBlock,
amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits ); amoebaGpu->energyOutputBuffers, (*gpu->psInteractionCount)[0], gpu->sim.workUnits );
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu
View file @ accc4ccd
...@@ -267,6 +267,7 @@ __device__ void calculateMutualInducedAndGkFieldsGkPairIxn_kernel( float4 atomCo ...@@ -267,6 +267,7 @@ __device__ void calculateMutualInducedAndGkFieldsGkPairIxn_kernel( float4 atomCo
} }
#ifdef AMOEBA_DEBUG
__device__ static int debugAccumulate( int index, float4* debugArray, float* field, unsigned int addMask, float idLabel ) __device__ static int debugAccumulate( int index, float4* debugArray, float* field, unsigned int addMask, float idLabel )
{ {
index += cAmoebaSim.paddedNumberOfAtoms; index += cAmoebaSim.paddedNumberOfAtoms;
...@@ -277,6 +278,7 @@ __device__ static int debugAccumulate( int index, float4* debugArray, float* fie ...@@ -277,6 +278,7 @@ __device__ static int debugAccumulate( int index, float4* debugArray, float* fie
return index; return index;
} }
#endif
#define GK #define GK
#include "kCalculateAmoebaCudaMutualInducedParticle.h" #include "kCalculateAmoebaCudaMutualInducedParticle.h"
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaWcaDispersion.cu
View file @ accc4ccd
...@@ -31,7 +31,7 @@ void GetCalculateAmoebaCudaWcaDispersionSim(amoebaGpuContext amoebaGpu) ...@@ -31,7 +31,7 @@ void GetCalculateAmoebaCudaWcaDispersionSim(amoebaGpuContext amoebaGpu)
gpuContext gpu = amoebaGpu->gpuContext; gpuContext gpu = amoebaGpu->gpuContext;
status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation)); status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));
fprintf( stderr, "In GetCalculateAmoebaCudaWcaDispersionSim: %p %u %u\n", fprintf( stderr, "In GetCalculateAmoebaCudaWcaDispersionSim: %p %lu %u\n",
gpu->psInteractionCount->_pSysStream[0], gpu->psInteractionCount->_pSysStream[0][0], gpu->sim.workUnits ); gpu->psInteractionCount->_pSysStream[0], gpu->psInteractionCount->_pSysStream[0][0], gpu->sim.workUnits );
RTERROR(status, "GetCalculateAmoebaCudaWcaDispersionSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed"); RTERROR(status, "GetCalculateAmoebaCudaWcaDispersionSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed");
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ accc4ccd
...@@ -306,7 +306,7 @@ static int setDoubleFromMap( MapStringString& argumentMap, std::string fieldToCh ...@@ -306,7 +306,7 @@ static int setDoubleFromMap( MapStringString& argumentMap, std::string fieldToCh
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
static char* readLine( FILE* filePtr, StringVector& tokens, int* lineCount, FILE* log ){ static int readLine( FILE* filePtr, StringVector& tokens, int* lineCount, FILE* log ){
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -323,7 +323,7 @@ static char* readLine( FILE* filePtr, StringVector& tokens, int* lineCount, FILE ...@@ -323,7 +323,7 @@ static char* readLine( FILE* filePtr, StringVector& tokens, int* lineCount, FILE
(*lineCount)++; (*lineCount)++;
tokenizeString( buffer, tokens, delimiter ); tokenizeString( buffer, tokens, delimiter );
} }
return isNotEof; return 0;
} }
...@@ -367,7 +367,7 @@ static int readFile( std::string fileName, StringVectorVector& fileContents, FIL ...@@ -367,7 +367,7 @@ static int readFile( std::string fileName, StringVectorVector& fileContents, FIL
StringVector firstLine; StringVector firstLine;
int lineCount = 0; int lineCount = 0;
char* isNotEof = readLine( filePtr, firstLine, &lineCount, log ); int isNotEof = readLine( filePtr, firstLine, &lineCount, log );
fileContents.push_back( firstLine ); fileContents.push_back( firstLine );
while( isNotEof ){ while( isNotEof ){
StringVector lineTokens; StringVector lineTokens;
...@@ -418,7 +418,7 @@ static int readVectorOfDoubleVectors( FILE* filePtr, const StringVector& tokens, ...@@ -418,7 +418,7 @@ static int readVectorOfDoubleVectors( FILE* filePtr, const StringVector& tokens,
for( int ii = 0; ii < numberToRead; ii++ ){ for( int ii = 0; ii < numberToRead; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 1 ){ if( lineTokens.size() > 1 ){
int index = atoi( lineTokens[0].c_str() ); int index = atoi( lineTokens[0].c_str() );
std::vector<double> nextEntry; std::vector<double> nextEntry;
...@@ -497,7 +497,7 @@ static int readVectorOfIntVectors( FILE* filePtr, const StringVector& tokens, st ...@@ -497,7 +497,7 @@ static int readVectorOfIntVectors( FILE* filePtr, const StringVector& tokens, st
} }
for( int ii = 0; ii < numberToRead; ii++ ){ for( int ii = 0; ii < numberToRead; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 1 ){ if( lineTokens.size() > 1 ){
int index = atoi( lineTokens[0].c_str() ); int index = atoi( lineTokens[0].c_str() );
std::vector<int> nextEntry; std::vector<int> nextEntry;
...@@ -659,7 +659,7 @@ static int readMasses( FILE* filePtr, const StringVector& tokens, System& system ...@@ -659,7 +659,7 @@ static int readMasses( FILE* filePtr, const StringVector& tokens, System& system
} }
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() >= 1 ){ if( lineTokens.size() >= 1 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -744,7 +744,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM ...@@ -744,7 +744,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
} }
for( int ii = 0; ii < numberOfBonds; ii++ ){ for( int ii = 0; ii < numberOfBonds; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 4 ){ if( lineTokens.size() > 4 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -761,7 +761,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM ...@@ -761,7 +761,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
// get cubic and quartic factors // get cubic and quartic factors
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 2 ){ while( hits < 2 ){
StringVector tokens; StringVector tokens;
...@@ -885,7 +885,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force ...@@ -885,7 +885,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
} }
for( int ii = 0; ii < numberOfAngles; ii++ ){ for( int ii = 0; ii < numberOfAngles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 5 ){ if( lineTokens.size() > 5 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -904,7 +904,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force ...@@ -904,7 +904,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
// get cubic, quartic, pentic, sextic factors // get cubic, quartic, pentic, sextic factors
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 4 ){ while( hits < 4 ){
StringVector tokens; StringVector tokens;
...@@ -1047,7 +1047,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt ...@@ -1047,7 +1047,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
} }
for( int ii = 0; ii < numberOfAngles; ii++ ){ for( int ii = 0; ii < numberOfAngles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 6 ){ if( lineTokens.size() > 6 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -1066,7 +1066,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt ...@@ -1066,7 +1066,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
// get cubic, quartic, pentic, sextic factors // get cubic, quartic, pentic, sextic factors
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 4 ){ while( hits < 4 ){
StringVector tokens; StringVector tokens;
...@@ -1208,7 +1208,7 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -1208,7 +1208,7 @@ static int readAmoebaTorsionParameters( FILE* filePtr, MapStringInt& forceMap, c
} }
for( int ii = 0; ii < numberOfTorsions; ii++ ){ for( int ii = 0; ii < numberOfTorsions; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 10 ){ if( lineTokens.size() > 10 ){
std::vector<double> torsion1; std::vector<double> torsion1;
std::vector<double> torsion2; std::vector<double> torsion2;
...@@ -1364,7 +1364,7 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -1364,7 +1364,7 @@ static int readAmoebaPiTorsionParameters( FILE* filePtr, MapStringInt& forceMap,
} }
for( int ii = 0; ii < numberOfPiTorsions; ii++ ){ for( int ii = 0; ii < numberOfPiTorsions; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 7 ){ if( lineTokens.size() > 7 ){
std::vector<double> torsionK; std::vector<double> torsionK;
int index = 0; int index = 0;
...@@ -1497,7 +1497,7 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa ...@@ -1497,7 +1497,7 @@ static int readAmoebaStretchBendParameters( FILE* filePtr, MapStringInt& forceMa
} }
for( int ii = 0; ii < numberOfStretchBends; ii++ ){ for( int ii = 0; ii < numberOfStretchBends; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 7 ){ if( lineTokens.size() > 7 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -1629,7 +1629,7 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc ...@@ -1629,7 +1629,7 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
} }
for( int ii = 0; ii < numberOfOutOfPlaneBends; ii++ ){ for( int ii = 0; ii < numberOfOutOfPlaneBends; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 5 ){ if( lineTokens.size() > 5 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -1647,7 +1647,7 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc ...@@ -1647,7 +1647,7 @@ static int readAmoebaOutOfPlaneBendParameters( FILE* filePtr, MapStringInt& forc
// get cubic, quartic, pentic, sextic factors // get cubic, quartic, pentic, sextic factors
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 4 ){ while( hits < 4 ){
StringVector tokens; StringVector tokens;
...@@ -1784,7 +1784,7 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors ...@@ -1784,7 +1784,7 @@ static int readAmoebaTorsionTorsionGrid( FILE* filePtr, int numX, int numY, Tors
} }
for( int ii = 0; ii < gridCount; ii++ ){ for( int ii = 0; ii < gridCount; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 8 ){ if( lineTokens.size() > 8 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -1924,7 +1924,7 @@ static int readAmoebaTorsionTorsionParameters( FILE* filePtr, MapStringInt& forc ...@@ -1924,7 +1924,7 @@ static int readAmoebaTorsionTorsionParameters( FILE* filePtr, MapStringInt& forc
} }
for( int ii = 0; ii < numberOfTorsionTorsions; ii++ ){ for( int ii = 0; ii < numberOfTorsionTorsions; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 7 ){ if( lineTokens.size() > 7 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -1944,7 +1944,7 @@ static int readAmoebaTorsionTorsionParameters( FILE* filePtr, MapStringInt& forc ...@@ -1944,7 +1944,7 @@ static int readAmoebaTorsionTorsionParameters( FILE* filePtr, MapStringInt& forc
// get grid // get grid
char* isNotEof = "1"; int isNotEof = 1;
int totalNumberOfGrids = 1; int totalNumberOfGrids = 1;
int gridCount = 0; int gridCount = 0;
while( gridCount < totalNumberOfGrids ){ while( gridCount < totalNumberOfGrids ){
...@@ -2039,7 +2039,7 @@ static void readAmoebaMultipoleCovalent( FILE* filePtr, AmoebaMultipoleForce* mu ...@@ -2039,7 +2039,7 @@ static void readAmoebaMultipoleCovalent( FILE* filePtr, AmoebaMultipoleForce* mu
AmoebaMultipoleForce::PolarizationCovalent13, AmoebaMultipoleForce::PolarizationCovalent13,
AmoebaMultipoleForce::PolarizationCovalent14 }; AmoebaMultipoleForce::PolarizationCovalent14 };
char* isNotEof = "1"; int isNotEof = 1;
for( int ii = 0; ii < numberOfMultipoles && isNotEof; ii++ ){ for( int ii = 0; ii < numberOfMultipoles && isNotEof; ii++ ){
for( unsigned int jj = 0; jj < numberOfCovalentTypes && isNotEof; jj++ ){ for( unsigned int jj = 0; jj < numberOfCovalentTypes && isNotEof; jj++ ){
StringVector lineTokens; StringVector lineTokens;
...@@ -2109,7 +2109,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2109,7 +2109,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
} }
for( int ii = 0; ii < numberOfMultipoles; ii++ ){ for( int ii = 0; ii < numberOfMultipoles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 7 ){ if( lineTokens.size() > 7 ){
std::vector<double> dipole; std::vector<double> dipole;
std::vector<double> quadrupole; std::vector<double> quadrupole;
...@@ -2146,7 +2146,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2146,7 +2146,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
// get supplementary fields // get supplementary fields
char* isNotEof = "1"; int isNotEof = 1;
int totalFields = 2; int totalFields = 2;
int fieldCount = 0; int fieldCount = 0;
int done = 0; int done = 0;
...@@ -2199,7 +2199,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2199,7 +2199,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
if( log ){ if( log ){
(void) fprintf( log, "%s Supplementary fields %u: ", methodName.c_str(), supplementary.size() ); (void) fprintf( log, "%s Supplementary fields %u: ", methodName.c_str(), static_cast<unsigned int>(supplementary.size()) );
for( MapStringVectorOfVectorsCI ii = supplementary.begin(); ii != supplementary.end(); ii++ ){ for( MapStringVectorOfVectorsCI ii = supplementary.begin(); ii != supplementary.end(); ii++ ){
(void) fprintf( log, "%s ", (*ii).first.c_str() ); (void) fprintf( log, "%s ", (*ii).first.c_str() );
} }
...@@ -2241,7 +2241,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap, ...@@ -2241,7 +2241,7 @@ static int readAmoebaMultipoleParameters( FILE* filePtr, MapStringInt& forceMap,
for( int jj = 0; jj < AmoebaMultipoleForce::CovalentEnd; jj++ ){ for( int jj = 0; jj < AmoebaMultipoleForce::CovalentEnd; jj++ ){
std::vector<int> covalentAtoms; std::vector<int> covalentAtoms;
multipoleForce->getCovalentMap( ii, covalentTypes[jj], covalentAtoms ); multipoleForce->getCovalentMap( ii, covalentTypes[jj], covalentAtoms );
(void) fprintf( log, " CovTypeId=%d %u [", jj, covalentAtoms.size() ); (void) fprintf( log, " CovTypeId=%d %u [", jj, static_cast<unsigned int>(covalentAtoms.size()) );
for( unsigned int kk = 0; kk < covalentAtoms.size(); kk++ ){ for( unsigned int kk = 0; kk < covalentAtoms.size(); kk++ ){
(void) fprintf( log, "%5d ", covalentAtoms[kk] ); (void) fprintf( log, "%5d ", covalentAtoms[kk] );
} }
...@@ -2364,7 +2364,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2364,7 +2364,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
} }
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
int tokenIndex = 0; int tokenIndex = 0;
if( lineTokens.size() > 3 ){ if( lineTokens.size() > 3 ){
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -2380,7 +2380,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2380,7 +2380,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
} }
} }
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 2 ){ while( hits < 2 ){
StringVector tokens; StringVector tokens;
...@@ -2396,13 +2396,13 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2396,13 +2396,13 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
hits++; hits++;
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s read past GK block at line=%d\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s read past GK block at line=%d\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
...@@ -2410,7 +2410,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt& ...@@ -2410,7 +2410,7 @@ static int readAmoebaGeneralizedKirkwoodParameters( FILE* filePtr, MapStringInt&
// get supplementart fields // get supplementart fields
isNotEof = "1"; isNotEof = 1;
int totalFields = 2; int totalFields = 2;
int fieldCount = 0; int fieldCount = 0;
int done = 0; int done = 0;
...@@ -2551,7 +2551,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2551,7 +2551,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
vdwForce->setSigEpsTableSize( tableSize ); vdwForce->setSigEpsTableSize( tableSize );
for( int ii = 0; ii < tableSize; ii++ ){ for( int ii = 0; ii < tableSize; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 2 ){ if( lineTokens.size() > 2 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -2569,7 +2569,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2569,7 +2569,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
} }
StringVector lineTokensT; StringVector lineTokensT;
char* isNotEof = readLine( filePtr, lineTokensT, lineCount, log ); int isNotEof = readLine( filePtr, lineTokensT, lineCount, log );
numberOfParticles = atoi( lineTokensT[1].c_str() ); numberOfParticles = atoi( lineTokensT[1].c_str() );
} else { } else {
numberOfParticles = atoi( tokens[1].c_str() ); numberOfParticles = atoi( tokens[1].c_str() );
...@@ -2582,7 +2582,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2582,7 +2582,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
} }
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 2 ){ if( lineTokens.size() > 2 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -2605,7 +2605,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2605,7 +2605,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
// abort if have changed // abort if have changed
StringVector lineTokensT; StringVector lineTokensT;
char* isNotEof = readLine( filePtr, lineTokensT, lineCount, log ); int isNotEof = readLine( filePtr, lineTokensT, lineCount, log );
if( lineTokensT[0] == "AmoebaVdw14_7Scales" ){ if( lineTokensT[0] == "AmoebaVdw14_7Scales" ){
int tokenIndex = 1; int tokenIndex = 1;
double scale2 = atof( lineTokensT[tokenIndex++].c_str() ); double scale2 = atof( lineTokensT[tokenIndex++].c_str() );
...@@ -2631,7 +2631,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2631,7 +2631,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
int numberOfParticles = atoi( lineTokensT[1].c_str() ); int numberOfParticles = atoi( lineTokensT[1].c_str() );
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
std::vector< int > exclusions; std::vector< int > exclusions;
if( lineTokens.size() > 1 ){ if( lineTokens.size() > 1 ){
int tokenIndex = 0; int tokenIndex = 0;
...@@ -2725,7 +2725,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const ...@@ -2725,7 +2725,7 @@ static int readAmoebaVdwParameters( FILE* filePtr, MapStringInt& forceMap, const
(void) fprintf( log, "%8d %8d %8d sig=[%10.4f %10.4f] eps=[ %10.4f %10.4f] redct=%10.4f ", (void) fprintf( log, "%8d %8d %8d sig=[%10.4f %10.4f] eps=[ %10.4f %10.4f] redct=%10.4f ",
ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction ); ii, indexIV, indexClass, sigma, sigma4, epsilon, epsilon4, reduction );
(void) fprintf( log, "Excl=%3u [", exclusions.size() ); (void) fprintf( log, "Excl=%3u [", static_cast<unsigned int>(exclusions.size()) );
for( unsigned int jj = 0; jj < exclusions.size(); jj++ ){ for( unsigned int jj = 0; jj < exclusions.size(); jj++ ){
(void) fprintf( log, "%5d ", exclusions[jj] ); (void) fprintf( log, "%5d ", exclusions[jj] );
} }
...@@ -2867,7 +2867,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2867,7 +2867,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
std::vector<double> maxDispersionEnergyVector; std::vector<double> maxDispersionEnergyVector;
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 2 ){ if( lineTokens.size() > 2 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -2886,7 +2886,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2886,7 +2886,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
} }
} }
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 6 ){ while( hits < 6 ){
StringVector tokens; StringVector tokens;
...@@ -2915,13 +2915,13 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2915,13 +2915,13 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
hits++; hits++;
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s read past WcaDispersion block at line=%d\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s read past WcaDispersion block at line=%d\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
...@@ -2971,7 +2971,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force ...@@ -2971,7 +2971,7 @@ static int readAmoebaWcaDispersionParameters( FILE* filePtr, MapStringInt& force
wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy ); wcaDispersionForce->getMaximumDispersionEnergy( ii, maxDispersionEnergy );
double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] ); double delta = fabs( maxDispersionEnergy - maxDispersionEnergyVector[ii] );
if( delta > 1.0e-05 ){ if( delta > 1.0e-05 ){
(void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f XXX\n" ); (void) fprintf( log, " maxDispEDiff=%12.5e %14.7f %14.7f XXX\n", delta, maxDispersionEnergy, maxDispersionEnergyVector[ii] );
errors++; errors++;
} }
} }
...@@ -3101,7 +3101,7 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -3101,7 +3101,7 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c
} }
for( int ii = 0; ii < numberOfParticles; ii++ ){ for( int ii = 0; ii < numberOfParticles; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 2 ){ if( lineTokens.size() > 2 ){
int tokenIndex = 0; int tokenIndex = 0;
int index = atoi( lineTokens[tokenIndex++].c_str() ); int index = atoi( lineTokens[tokenIndex++].c_str() );
...@@ -3114,7 +3114,7 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -3114,7 +3114,7 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c
} }
} }
char* isNotEof = "1"; int isNotEof = 1;
int hits = 0; int hits = 0;
while( hits < 1 ){ while( hits < 1 ){
StringVector tokens; StringVector tokens;
...@@ -3127,13 +3127,13 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c ...@@ -3127,13 +3127,13 @@ static int readAmoebaSurfaceParameters( FILE* filePtr, MapStringInt& forceMap, c
hits++; hits++;
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s read past SASA block at line=%d\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s read past SASA block at line=%d\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
} else { } else {
char buffer[1024]; char buffer[1024];
(void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), lineCount ); (void) sprintf( buffer, "%s invalid token count at line=%d?\n", methodName.c_str(), *lineCount );
throwException(__FILE__, __LINE__, buffer ); throwException(__FILE__, __LINE__, buffer );
exit(-1); exit(-1);
} }
...@@ -3204,7 +3204,7 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s ...@@ -3204,7 +3204,7 @@ static int readConstraints( FILE* filePtr, const StringVector& tokens, System& s
} }
for( int ii = 0; ii < numberOfConstraints; ii++ ){ for( int ii = 0; ii < numberOfConstraints; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 3 ){ if( lineTokens.size() > 3 ){
int index = atoi( lineTokens[0].c_str() ); int index = atoi( lineTokens[0].c_str() );
int particle1 = atoi( lineTokens[1].c_str() ); int particle1 = atoi( lineTokens[1].c_str() );
...@@ -3313,7 +3313,7 @@ static Integrator* readIntegrator( FILE* filePtr, const StringVector& tokens, Sy ...@@ -3313,7 +3313,7 @@ static Integrator* readIntegrator( FILE* filePtr, const StringVector& tokens, Sy
for( int ii = 0; ii < readLines; ii++ ){ for( int ii = 0; ii < readLines; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 1 ){ if( lineTokens.size() > 1 ){
if( lineTokens[0] == "StepSize" ){ if( lineTokens[0] == "StepSize" ){
stepSize = atof( lineTokens[1].c_str() ); stepSize = atof( lineTokens[1].c_str() );
...@@ -3418,7 +3418,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3 ...@@ -3418,7 +3418,7 @@ static int readVec3( FILE* filePtr, const StringVector& tokens, std::vector<Vec3
} }
for( int ii = 0; ii < numberOfCoordinates; ii++ ){ for( int ii = 0; ii < numberOfCoordinates; ii++ ){
StringVector lineTokens; StringVector lineTokens;
char* isNotEof = readLine( filePtr, lineTokens, lineCount, log ); int isNotEof = readLine( filePtr, lineTokens, lineCount, log );
if( lineTokens.size() > 3 ){ if( lineTokens.size() > 3 ){
int index = atoi( lineTokens[0].c_str() ); int index = atoi( lineTokens[0].c_str() );
double xCoord = atof( lineTokens[1].c_str() ); double xCoord = atof( lineTokens[1].c_str() );
...@@ -3733,7 +3733,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS ...@@ -3733,7 +3733,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
int lineCount = 0; int lineCount = 0;
std::string version = "0.1"; std::string version = "0.1";
char* isNotEof = "1"; int isNotEof = 1;
Integrator* returnIntegrator = NULL; Integrator* returnIntegrator = NULL;
// loop over lines in file // loop over lines in file
...@@ -4561,9 +4561,12 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr ...@@ -4561,9 +4561,12 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "createContext"; static const std::string methodName = "createContext";
int cudaDevice = -1;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
setIntFromMap( inputArgumentMap, "cudaDevice", cudaDevice );
System* system = new System(); System* system = new System();
std::vector<Vec3> coordinates; std::vector<Vec3> coordinates;
...@@ -4583,7 +4586,22 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr ...@@ -4583,7 +4586,22 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr
tinkerForces, tinkerEnergies, supplementary, useOpenMMUnits, inputArgumentMap, log ); tinkerForces, tinkerEnergies, supplementary, useOpenMMUnits, inputArgumentMap, log );
Integrator* integrator = getIntegrator( inputArgumentMap, log ); Integrator* integrator = getIntegrator( inputArgumentMap, log );
Context* context = new Context(*system, *integrator, Platform::getPlatformByName( "Cuda"));
Context* context;
if( getenv("CudaDevice") || cudaDevice > -1 ){
Platform& platform = Platform::getPlatformByName("Cuda");
map<string, string> properties;
if( getenv("CudaDevice") ){
properties["CudaDevice"] = getenv("CudaDevice");
} else {
std::stringstream cudaDeviceStrStr;
cudaDeviceStrStr << cudaDevice;
properties["CudaDevice"] = cudaDeviceStrStr.str();
}
context = new Context(*system, *integrator, platform, properties);
} else {
context = new Context(*system, *integrator, Platform::getPlatformByName( "Cuda"));
}
context->setPositions(coordinates); context->setPositions(coordinates);
return context; return context;
...@@ -4679,7 +4697,7 @@ fprintf( log, "\n" ); fflush( log ); */ ...@@ -4679,7 +4697,7 @@ fprintf( log, "\n" ); fflush( log ); */
if( skip ){ if( skip ){
(void) fprintf( log, "Skipping state=%u line=%u\n", stateIndex, lineIndex ); (void) fprintf( log, "Skipping state=%u line=%u\n", stateIndex, lineIndex );
} else { } else {
(void) fprintf( log, "State=%u coordinates=%u\n", stateIndex, coordinates.size() ); (void) fprintf( log, "State=%u coordinates=%u\n", stateIndex, static_cast<unsigned int>(coordinates.size()) );
context->setPositions( coordinates ); context->setPositions( coordinates );
State state = context->getState(State::Forces | State::Energy); State state = context->getState(State::Forces | State::Energy);
System& system = context->getSystem(); System& system = context->getSystem();
...@@ -4820,7 +4838,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete ...@@ -4820,7 +4838,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
deltaE, expectedEnergy, energyConversion*state.getPotentialEnergy(), deltaE, expectedEnergy, energyConversion*state.getPotentialEnergy(),
amoebaTinkerParameterFileName.c_str(), activeForceNames.c_str() ); amoebaTinkerParameterFileName.c_str(), activeForceNames.c_str() );
(void) fprintf( filePtr, "%s: %u %u Active forces: %s\n", (void) fprintf( filePtr, "%s: %u %u Active forces: %s\n",
methodName.c_str(), expectedForces.size(), forces.size(), activeForceNames.c_str() ); methodName.c_str(), static_cast<unsigned int>(expectedForces.size()), static_cast<unsigned int>(forces.size()), activeForceNames.c_str() );
double maxRelativeDelta = -1.0e+30; double maxRelativeDelta = -1.0e+30;
unsigned int maxRelativeDeltaIndex = -1; unsigned int maxRelativeDeltaIndex = -1;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){ for( unsigned int ii = 0; ii < forces.size(); ii++ ){
...@@ -4882,7 +4900,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete ...@@ -4882,7 +4900,7 @@ void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParamete
coordinateConversion*(box[1][2] - box[0][2]) ); coordinateConversion*(box[1][2] - box[0][2]) );
unsigned int maxPrint = 5; unsigned int maxPrint = 5;
(void) fprintf( filePtr, "Sample raw coordinates (w/o conversion) %8u\n", coordinates.size() ); (void) fprintf( filePtr, "Sample raw coordinates (w/o conversion) %8u\n", static_cast<unsigned int>(coordinates.size()) );
for( unsigned int ii = 0; ii < coordinates.size(); ii++ ){ for( unsigned int ii = 0; ii < coordinates.size(); ii++ ){
(void) fprintf( filePtr, "%8u [%16.7f %16.7f %16.7f]\n", ii, (void) fprintf( filePtr, "%8u [%16.7f %16.7f %16.7f]\n", ii,
coordinates[ii][0], coordinates[ii][1], coordinates[ii][2] ); coordinates[ii][0], coordinates[ii][1], coordinates[ii][2] );
...@@ -5263,7 +5281,7 @@ void writeIntermediateStateFile( Context& context, FILE* intermediateStateFile, ...@@ -5263,7 +5281,7 @@ void writeIntermediateStateFile( Context& context, FILE* intermediateStateFile,
const std::vector<Vec3> forces = state.getForces(); const std::vector<Vec3> forces = state.getForces();
(void) fprintf( intermediateStateFile, "%7u %12.3f %15.7e %15.7e %15.7e State (x,v,f)\n", (void) fprintf( intermediateStateFile, "%7u %12.3f %15.7e %15.7e %15.7e State (x,v,f)\n",
positions.size(), state.getTime(), state.getKineticEnergy(), state.getPotentialEnergy(), static_cast<unsigned int>(positions.size()), state.getTime(), state.getKineticEnergy(), state.getPotentialEnergy(),
state.getKineticEnergy() + state.getPotentialEnergy() ); state.getKineticEnergy() + state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){ for( unsigned int ii = 0; ii < positions.size(); ii++ ){
...@@ -5601,7 +5619,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM ...@@ -5601,7 +5619,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
(void) fprintf( log, "Final Simulation: %12.3f E=%15.7e [%15.7e %15.7e] total wall time=%12.3e ns/day=%.3e\n", (void) fprintf( log, "Final Simulation: %12.3f E=%15.7e [%15.7e %15.7e] total wall time=%12.3e ns/day=%.3e\n",
currentTime, (kineticEnergy + potentialEnergy), kineticEnergy, potentialEnergy, currentTime, (kineticEnergy + potentialEnergy), kineticEnergy, potentialEnergy,
totalWallClockTime, nsPerDay ); totalWallClockTime, nsPerDay );
(void) fprintf( log, "\n%8u Energies\n", kineticEnergyArray.size() ); (void) fprintf( log, "\n%8u Energies\n", static_cast<unsigned int>(kineticEnergyArray.size()) );
for( unsigned int ii = 0; ii < kineticEnergyArray.size(); ii++ ){ for( unsigned int ii = 0; ii < kineticEnergyArray.size(); ii++ ){
(void) fprintf( log, "%15.7e %15.7e %15.7e %15.7e Energies\n", (void) fprintf( log, "%15.7e %15.7e %15.7e %15.7e Energies\n",
timeArray[ii], kineticEnergyArray[ii], potentialEnergyArray[ii], totalEnergyArray[ii] ); timeArray[ii], kineticEnergyArray[ii], potentialEnergyArray[ii], totalEnergyArray[ii] );
...@@ -5803,7 +5821,7 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){ ...@@ -5803,7 +5821,7 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
} }
(void) fprintf( log, "parameter file=<%s>\n", parameterFileName.c_str() ); (void) fprintf( log, "parameter file=<%s>\n", parameterFileName.c_str() );
(void) fprintf( log, "Argument map: %u\n", inputArgumentMap.size() ); (void) fprintf( log, "Argument map: %u\n", static_cast<unsigned int>(inputArgumentMap.size()) );
for( MapStringStringCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){ for( MapStringStringCI ii = inputArgumentMap.begin(); ii != inputArgumentMap.end(); ii++ ){
(void) fprintf( log, "Map %s %s\n", (*ii).first.c_str(), (*ii).second.c_str() ); (void) fprintf( log, "Map %s %s\n", (*ii).first.c_str(), (*ii).second.c_str() );
} }
......
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