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Commit 12680294 authored by Mark Friedrichs's avatar Mark Friedrichs
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Fixed parameter scaling issue w/ AmoebaHarmonicBondForce 

Test use env variable OPENMM_PLUGIN_DIR to find plugin
parent 192670e9
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Showing with 220 additions and 87 deletions
plugins/amoeba/platforms/cuda/src/kernels/AmoebaGpu.cpp
View file @ 12680294
......@@ -212,8 +212,8 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
gpuPrintCudaStreamFloat2( amoebaGpu->psAmoebaBondParameter, log );
(void) fprintf( log, " amoebaBonds %u\n", amoebaGpu->amoebaSim.amoebaBonds );
(void) fprintf( log, " amoebaBond_offset %u\n", amoebaGpu->amoebaSim.amoebaBond_offset );
(void) fprintf( log, " cubic %14.7e\n", amoebaGpu->amoebaSim.amoebaBondCubicParameter);
(void) fprintf( log, " quartic %14.7e\n", amoebaGpu->amoebaSim.amoebaBondQuarticicParameter);
(void) fprintf( log, " cubic %15.7e\n", amoebaGpu->amoebaSim.amoebaBondCubicParameter);
(void) fprintf( log, " quartic %15.7e\n", amoebaGpu->amoebaSim.amoebaBondQuarticicParameter);
(void) fprintf( log, " pAmoebaBondID %p\n", amoebaGpu->amoebaSim.pAmoebaBondID );
(void) fprintf( log, " pAmoebaBondParameter %p\n", amoebaGpu->amoebaSim.pAmoebaBondParameter );
......@@ -223,10 +223,10 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, "\n" );
(void) fprintf( log, " amoebaAngles %u\n", amoebaGpu->amoebaSim.amoebaAngles );
(void) fprintf( log, " amoebaAngle_offset %u\n", amoebaGpu->amoebaSim.amoebaAngle_offset );
(void) fprintf( log, " amoebaAngleCubicK %14.7e\n", amoebaGpu->amoebaSim.amoebaAngleCubicK );
(void) fprintf( log, " amoebaAngleQuarticK %14.7e\n", amoebaGpu->amoebaSim.amoebaAngleQuarticK );
(void) fprintf( log, " amoebaAnglePenticK %14.7e\n", amoebaGpu->amoebaSim.amoebaAnglePenticK );
(void) fprintf( log, " amoebaAngleSexticK %14.7e\n", amoebaGpu->amoebaSim.amoebaAngleSexticK );
(void) fprintf( log, " amoebaAngleCubicK %15.7e\n", amoebaGpu->amoebaSim.amoebaAngleCubicK );
(void) fprintf( log, " amoebaAngleQuarticK %15.7e\n", amoebaGpu->amoebaSim.amoebaAngleQuarticK );
(void) fprintf( log, " amoebaAnglePenticK %15.7e\n", amoebaGpu->amoebaSim.amoebaAnglePenticK );
(void) fprintf( log, " amoebaAngleSexticK %15.7e\n", amoebaGpu->amoebaSim.amoebaAngleSexticK );
(void) fprintf( log, " pAmoebaAngleID1 %p\n", amoebaGpu->amoebaSim.pAmoebaAngleID1 );
(void) fprintf( log, " pAmoebaAngleID2 %p\n", amoebaGpu->amoebaSim.pAmoebaAngleID2 );
(void) fprintf( log, " pAmoebaAngleParameter %p\n", amoebaGpu->amoebaSim.pAmoebaAngleParameter );
......@@ -238,10 +238,10 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, "\n" );
(void) fprintf( log, " amoebaInPlaneAngles %u\n", amoebaGpu->amoebaSim.amoebaInPlaneAngles );
(void) fprintf( log, " amoebaInPlaneAngle_offset %u\n", amoebaGpu->amoebaSim.amoebaInPlaneAngle_offset );
(void) fprintf( log, " amoebaInPlaneAngleCubicK %14.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleCubicK );
(void) fprintf( log, " amoebaInPlaneAngleQuarticK %14.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleQuarticK );
(void) fprintf( log, " amoebaInPlaneAnglePenticK %14.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAnglePenticK );
(void) fprintf( log, " amoebaInPlaneAngleSexticK %14.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleSexticK );
(void) fprintf( log, " amoebaInPlaneAngleCubicK %15.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleCubicK );
(void) fprintf( log, " amoebaInPlaneAngleQuarticK %15.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleQuarticK );
(void) fprintf( log, " amoebaInPlaneAnglePenticK %15.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAnglePenticK );
(void) fprintf( log, " amoebaInPlaneAngleSexticK %15.7e\n", amoebaGpu->amoebaSim.amoebaInPlaneAngleSexticK );
(void) fprintf( log, " pAmoebaInPlaneAngleID1 %p\n", amoebaGpu->amoebaSim.pAmoebaInPlaneAngleID1 );
(void) fprintf( log, " pAmoebaInPlaneAngleID2 %p\n", amoebaGpu->amoebaSim.pAmoebaInPlaneAngleID2 );
(void) fprintf( log, " pAmoebaInPlaneAngleParameter %p\n", amoebaGpu->amoebaSim.pAmoebaInPlaneAngleParameter );
......@@ -288,10 +288,10 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
gpuPrintCudaStreamFloat( amoebaGpu->psAmoebaOutOfPlaneBendParameter, log );
(void) fprintf( log, " amoebaOutOfPlaneBend %u\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBends );
(void) fprintf( log, " amoebaOutOfPlaneBend_offset %u\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBend_offset );
(void) fprintf( log, " amoebaOutOfPlaneBendCubicK %14.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendCubicK );
(void) fprintf( log, " amoebaOutOfPlaneBendQuarticK %14.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendQuarticK );
(void) fprintf( log, " amoebaOutOfPlaneBendPenticK %14.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendPenticK );
(void) fprintf( log, " amoebaOutOfPlaneBendSexticK %14.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendSexticK );
(void) fprintf( log, " amoebaOutOfPlaneBendCubicK %15.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendCubicK );
(void) fprintf( log, " amoebaOutOfPlaneBendQuarticK %15.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendQuarticK );
(void) fprintf( log, " amoebaOutOfPlaneBendPenticK %15.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendPenticK );
(void) fprintf( log, " amoebaOutOfPlaneBendSexticK %15.7e\n", amoebaGpu->amoebaSim.amoebaOutOfPlaneBendSexticK );
(void) fprintf( log, " pAmoebaOutOfPlaneBendID1 %p\n", amoebaGpu->amoebaSim.pAmoebaOutOfPlaneBendID1 );
(void) fprintf( log, " pAmoebaOutOfPlaneBendID2 %p\n", amoebaGpu->amoebaSim.pAmoebaOutOfPlaneBendID2 );
(void) fprintf( log, " pAmoebaOutOfPlaneBendParameter %p\n", amoebaGpu->amoebaSim.pAmoebaOutOfPlaneBendParameter );
......@@ -323,19 +323,19 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
(void) fprintf( log, " solventDielectric %10.3f\n", amoebaGpu->solventDielectric);
(void) fprintf( log, " pGamma %10.3f\n", amoebaGpu->pGamma );
(void) fprintf( log, " scalingDistanceCutoff %10.3f\n", amoebaGpu->scalingDistanceCutoff );
(void) fprintf( log, " scalingDistanceCutoff %14.7e\n", amoebaGpu->amoebaSim.scalingDistanceCutoff );
(void) fprintf( log, " scalingDistanceCutoff %15.7e\n", amoebaGpu->amoebaSim.scalingDistanceCutoff );
(void) fprintf( log, " pDampingFactorAndThole %p\n", amoebaGpu->amoebaSim.pDampingFactorAndThole );
(void) fprintf( log, " pScaleIndicesIndex %p\n", amoebaGpu->amoebaSim.pScaleIndicesIndex );
(void) fprintf( log, " pD_ScaleIndices %p\n", amoebaGpu->amoebaSim.pD_ScaleIndices );
(void) fprintf( log, " pP_ScaleIndices %p\n", amoebaGpu->amoebaSim.pP_ScaleIndices );
(void) fprintf( log, " pM_ScaleIndices %p\n", amoebaGpu->amoebaSim.pM_ScaleIndices );
(void) fprintf( log, " electric %14.7e\n", amoebaGpu->amoebaSim.electric );
(void) fprintf( log, " gkc %14.7e\n", amoebaGpu->amoebaSim.gkc );
(void) fprintf( log, " dielec %14.7e\n", amoebaGpu->amoebaSim.dielec );
(void) fprintf( log, " dwater %14.7e\n", amoebaGpu->amoebaSim.dwater );
(void) fprintf( log, " fc %14.7e\n", amoebaGpu->amoebaSim.fc );
(void) fprintf( log, " fd %14.7e\n", amoebaGpu->amoebaSim.fd );
(void) fprintf( log, " fq %14.7e\n", amoebaGpu->amoebaSim.fq );
(void) fprintf( log, " electric %15.7e\n", amoebaGpu->amoebaSim.electric );
(void) fprintf( log, " gkc %15.7e\n", amoebaGpu->amoebaSim.gkc );
(void) fprintf( log, " dielec %15.7e\n", amoebaGpu->amoebaSim.dielec );
(void) fprintf( log, " dwater %15.7e\n", amoebaGpu->amoebaSim.dwater );
(void) fprintf( log, " fc %15.7e\n", amoebaGpu->amoebaSim.fc );
(void) fprintf( log, " fd %15.7e\n", amoebaGpu->amoebaSim.fd );
(void) fprintf( log, " fq %15.7e\n", amoebaGpu->amoebaSim.fq );
gpuPrintCudaStreamFloat2( amoebaGpu->psDampingFactorAndThole, log );
......@@ -375,9 +375,9 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
gpuPrintCudaStreamFloat( amoebaGpu->psKirkwoodForce, log );
gpuPrintCudaStreamFloat( amoebaGpu->psKirkwoodEDiffForce, log );
(void) fprintf( log, " includeObcCavityTerm %d\n", amoebaGpu->includeObcCavityTerm );
(void) fprintf( log, " dielectricOffset %14.7e\n", gpu->sim.dielectricOffset );
(void) fprintf( log, " probeRadius %14.7e\n", gpu->sim.probeRadius );
(void) fprintf( log, " surfaceAreaFactor %14.7e\n", gpu->sim.surfaceAreaFactor );
(void) fprintf( log, " dielectricOffset %15.7e\n", gpu->sim.dielectricOffset );
(void) fprintf( log, " probeRadius %15.7e\n", gpu->sim.probeRadius );
(void) fprintf( log, " surfaceAreaFactor %15.7e\n", gpu->sim.surfaceAreaFactor );
(void) fprintf( log, "\n" );
......@@ -404,14 +404,14 @@ void gpuPrintCudaAmoebaGmxSimulation(amoebaGpuContext amoebaGpu, FILE* log )
gpuPrintCudaStreamFloat2( amoebaGpu->psWcaDispersionRadiusEpsilon, log );
(void) fprintf( log, "\n" );
(void) fprintf( log, " epso %14.7e\n", amoebaGpu->amoebaSim.epso );
(void) fprintf( log, " epsh %14.7e\n", amoebaGpu->amoebaSim.epsh );
(void) fprintf( log, " rmino %14.7e\n", amoebaGpu->amoebaSim.rmino );
(void) fprintf( log, " rminh %14.7e\n", amoebaGpu->amoebaSim.rminh );
(void) fprintf( log, " awater %14.7e\n", amoebaGpu->amoebaSim.awater );
(void) fprintf( log, " shctd %14.7e\n", amoebaGpu->amoebaSim.shctd );
(void) fprintf( log, " dispoff %14.7e\n", amoebaGpu->amoebaSim.dispoff );
(void) fprintf( log, " totalMaxWcaDispersionEnergy %14.7e\n", amoebaGpu->amoebaSim.totalMaxWcaDispersionEnergy );
(void) fprintf( log, " epso %15.7e\n", amoebaGpu->amoebaSim.epso );
(void) fprintf( log, " epsh %15.7e\n", amoebaGpu->amoebaSim.epsh );
(void) fprintf( log, " rmino %15.7e\n", amoebaGpu->amoebaSim.rmino );
(void) fprintf( log, " rminh %15.7e\n", amoebaGpu->amoebaSim.rminh );
(void) fprintf( log, " awater %15.7e\n", amoebaGpu->amoebaSim.awater );
(void) fprintf( log, " shctd %15.7e\n", amoebaGpu->amoebaSim.shctd );
(void) fprintf( log, " dispoff %15.7e\n", amoebaGpu->amoebaSim.dispoff );
(void) fprintf( log, " totalMaxWcaDispersionEnergy %15.7e\n", amoebaGpu->amoebaSim.totalMaxWcaDispersionEnergy );
(void) fflush( log );
......@@ -448,7 +448,7 @@ void gpuSetAmoebaBondParameters(amoebaGpuContext amoebaGpu, const std::vector<in
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( amoebaGpu->log && (i < DUMP_PARAMETERS || i > bonds - (DUMP_PARAMETERS + 1) ) )
fprintf( amoebaGpu->log, "Bonds: %5d [%5d %5d %5d %5d] L=%14.7e k[%14.7e %14.7e %14.7e] [%5d %5d]\n",
fprintf( amoebaGpu->log, "Bonds: %5d [%5d %5d %5d %5d] L=%15.7e k[%15.7e %15.7e %15.7e] [%5d %5d]\n",
i, (*psBondID)[i].x, (*psBondID)[i].y, (*psBondID)[i].z, (*psBondID)[i].w,
(*psBondParameter)[i].x, (*psBondParameter)[i].y, cubic, quartic,
gpu->pOutputBufferCounter[(*psBondID)[i].x],
......@@ -503,7 +503,7 @@ void gpuSetAmoebaAngleParameters(amoebaGpuContext amoebaGpu, const std::vector<i
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > bond_angles - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "Angles: %5d [%5d %5d %5d] [%5d %5d %5d] A=%14.7e k[%14.7e %14.7e] [%5d %5d %5d]\n", i,
fprintf( amoebaGpu->log, "Angles: %5d [%5d %5d %5d] [%5d %5d %5d] A=%15.7e k[%15.7e %15.7e] [%5d %5d %5d]\n", i,
(*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w,
(*psAngleID2)[i].x, (*psAngleID2)[i].y,
(*psAngleParameter)[i].x, (*psAngleParameter)[i].y,
......@@ -563,7 +563,7 @@ void gpuSetAmoebaInPlaneAngleParameters(amoebaGpuContext amoebaGpu, const std::v
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
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=%14.7e k[%14.7e %14.7e %14.7e %14.7e %14.7e] [%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 %15.7e %15.7e %15.7e %15.7e] [%5d %5d %5d %5d]\n", i,
(*psAngleID1)[i].x, (*psAngleID1)[i].y, (*psAngleID1)[i].z, (*psAngleID1)[i].w,
(*psAngleID2)[i].x, (*psAngleID2)[i].y, (*psAngleID2)[i].z, (*psAngleID2)[i].w,
(*psAngleParameter)[i].x, (*psAngleParameter)[i].y,
......@@ -632,7 +632,7 @@ void gpuSetAmoebaTorsionParameters(amoebaGpuContext amoebaGpu, const std::vector
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > torsions - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "Torsions: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] 0[%14.7e %14.7e] 1[%14.7e %14.7e] 2[%14.7e %14.7e] [%5d %5d %5d %5d]\n", i,
fprintf( amoebaGpu->log, "Torsions: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] 0[%15.7e %15.7e] 1[%15.7e %15.7e] 2[%15.7e %15.7e] [%5d %5d %5d %5d]\n", i,
(*psTorsionID1)[i].x, (*psTorsionID1)[i].y, (*psTorsionID1)[i].z, (*psTorsionID1)[i].w,
(*psTorsionID2)[i].x, (*psTorsionID2)[i].y, (*psTorsionID2)[i].z, (*psTorsionID2)[i].w,
(*psTorsionParameter1)[i].x, (*psTorsionParameter1)[i].y, (*psTorsionParameter1)[i].z, (*psTorsionParameter1)[i].w,
......@@ -700,7 +700,7 @@ void gpuSetAmoebaPiTorsionParameters(amoebaGpuContext amoebaGpu, const std::vect
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > piTorsions - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "PiTorsions: %5d [%5d %5d %5d %5d %5d %5d [%5d %5d %5d %5d %5d %5d] k=%14.7e [%5d %5d %5d %5d %5d %5d]\n", i,
fprintf( amoebaGpu->log, "PiTorsions: %5d [%5d %5d %5d %5d %5d %5d [%5d %5d %5d %5d %5d %5d] k=%15.7e [%5d %5d %5d %5d %5d %5d]\n", i,
(*psPiTorsionID1)[i].x, (*psPiTorsionID1)[i].y, (*psPiTorsionID1)[i].z, (*psPiTorsionID1)[i].w,
(*psPiTorsionID2)[i].x, (*psPiTorsionID2)[i].y, (*psPiTorsionID2)[i].z, (*psPiTorsionID2)[i].w,
(*psPiTorsionID3)[i].x, (*psPiTorsionID3)[i].y, (*psPiTorsionID3)[i].z, (*psPiTorsionID3)[i].w,
......@@ -760,7 +760,7 @@ void gpuSetAmoebaStretchBendParameters(amoebaGpuContext amoebaGpu, const std::ve
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > stretchBends - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "StretchBends: %5d [%5d %5d %5d] [%5d %5d %5d] [%14.7e %14.7e %14.7e %14.7e [%5d %5d %5d]\n", i,
fprintf( amoebaGpu->log, "StretchBends: %5d [%5d %5d %5d] [%5d %5d %5d] [%15.7e %15.7e %15.7e %15.7e [%5d %5d %5d]\n", i,
(*psStretchBendID1)[i].x, (*psStretchBendID1)[i].y, (*psStretchBendID1)[i].z, (*psStretchBendID1)[i].w,
(*psStretchBendID2)[i].x, (*psStretchBendID2)[i].y,
(*psStretchBendParameter)[i].x, (*psStretchBendParameter)[i].y, (*psStretchBendParameter)[i].z, (*psStretchBendParameter)[i].w,
......@@ -806,7 +806,7 @@ void gpuSetAmoebaOutOfPlaneBendParameters(amoebaGpuContext amoebaGpu, const std:
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( amoebaGpu->log )
fprintf( amoebaGpu->log, "OutOfPlaneBends: global ks[%14.7e %14.7e %14.7e %14.7e]\n", cubicK, quarticK, penticK, sexticK );
fprintf( amoebaGpu->log, "OutOfPlaneBends: global ks[%15.7e %15.7e %15.7e %15.7e]\n", cubicK, quarticK, penticK, sexticK );
#endif
for (int i = 0; i < outOfPlaneBends; i++)
......@@ -823,7 +823,7 @@ void gpuSetAmoebaOutOfPlaneBendParameters(amoebaGpuContext amoebaGpu, const std:
#if (DUMP_PARAMETERS > 0 )
if( (i < DUMP_PARAMETERS || i > outOfPlaneBends - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "OutOfPlaneBends: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] k=%14.7e [%5d %5d %5d %5d]\n", i,
fprintf( amoebaGpu->log, "OutOfPlaneBends: %5d [%5d %5d %5d %5d] [%5d %5d %5d %5d] k=%15.7e [%5d %5d %5d %5d]\n", i,
(*psOutOfPlaneBendID1)[i].x, (*psOutOfPlaneBendID1)[i].y, (*psOutOfPlaneBendID1)[i].z, (*psOutOfPlaneBendID1)[i].w,
(*psOutOfPlaneBendID2)[i].x, (*psOutOfPlaneBendID2)[i].y, (*psOutOfPlaneBendID2)[i].z, (*psOutOfPlaneBendID2)[i].w,
(*psOutOfPlaneBendParameter)[i],
......@@ -957,7 +957,7 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vect
#define DUMP_PARAMETERS 5
#if (DUMP_PARAMETERS > 0 )
if( (index < DUMP_PARAMETERS || index > totalEntries - (DUMP_PARAMETERS + 1)) && amoebaGpu->log )
fprintf( amoebaGpu->log, "TorsionTorsionGrid: %d %5d [%5d %5d ] [%10.3f %10.3f] [%14.7e %14.7e %14.7e %14.7e]\n", index, ii, jj, kk,
fprintf( amoebaGpu->log, "TorsionTorsionGrid: %d %5d [%5d %5d ] [%10.3f %10.3f] [%15.7e %15.7e %15.7e %15.7e]\n", index, ii, jj, kk,
floatGrids[ii][jj][kk][0], floatGrids[ii][jj][kk][1],
(*psTorsionTorsionGrids)[index].x, (*psTorsionTorsionGrids)[index].y, (*psTorsionTorsionGrids)[index].z, (*psTorsionTorsionGrids)[index].w );
#endif
......@@ -1004,7 +1004,7 @@ if( (index < DUMP_PARAMETERS || index > totalEntries - (DUMP_PARAMETERS + 1)) &&
fabsf( values[1] - floatGrids[ii][jj][kk][3] ) > epsilon ||
fabsf( values[2] - floatGrids[ii][jj][kk][4] ) > epsilon ||
fabsf( values[3] - floatGrids[ii][jj][kk][5] ) > epsilon ){
(void) fprintf( amoebaGpu->log, "Error %u %u %u [%10.3f %10.3f] [%14.7e %14.7e %14.7e %14.7e] lk=[%14.7e %14.7e %14.7e %14.7e]\n", ii, jj, kk,
(void) fprintf( amoebaGpu->log, "Error %u %u %u [%10.3f %10.3f] [%15.7e %15.7e %15.7e %15.7e] lk=[%15.7e %15.7e %15.7e %15.7e]\n", ii, jj, kk,
floatGrids[ii][jj][kk][0], floatGrids[ii][jj][kk][1],
floatGrids[ii][jj][kk][2], floatGrids[ii][jj][kk][3], floatGrids[ii][jj][kk][4], floatGrids[ii][jj][kk][5],
values[0], values[1], values[2], values[3] );
......@@ -2113,7 +2113,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
amoebaGpu->vdwSigmaCombiningRule, amoebaGpu->vdwEpsilonCombiningRule);
for (unsigned int ii = 0; ii < gpu->natoms; ii++)
{
(void) fprintf( amoebaGpu->log, "%5u %14.7e %14.7e\n", ii, sigmas[ii], epsilons[ii] );
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, sigmas[ii], epsilons[ii] );
if( ii == maxPrint && ii < (amoebaGpu->paddedNumberOfAtoms - maxPrint) )
{
ii = (amoebaGpu->paddedNumberOfAtoms - maxPrint);
......@@ -2409,7 +2409,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
methodName, radii.size(), totalMaxWcaDisperionEnergy, epso, epsh, rmino, rminh, awater, shctd, dispoff );
for (unsigned int ii = 0; ii < gpu->natoms; ii++)
{
(void) fprintf( amoebaGpu->log, "%5u %14.7e %14.7e\n", ii, radii[ii], epsilons[ii] );
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, radii[ii], epsilons[ii] );
if( ii == maxPrint && ii < (amoebaGpu->paddedNumberOfAtoms - maxPrint) )
{
ii = (amoebaGpu->paddedNumberOfAtoms - maxPrint);
......@@ -2476,7 +2476,7 @@ float scaleRadius = 10.0f;
(void) fprintf( amoebaGpu->log, "%s probeRadius=%12.3f\n", methodName, probeRadius );
for (unsigned int ii = 0; ii < gpu->natoms; ii++)
{
(void) fprintf( amoebaGpu->log, "%5u %14.7e %14.7e\n", ii, radii[ii], weights[ii] );
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, radii[ii], weights[ii] );
if( ii == maxPrint && ii < (amoebaGpu->paddedNumberOfAtoms - maxPrint) )
{
ii = (amoebaGpu->paddedNumberOfAtoms - maxPrint);
......
plugins/amoeba/platforms/cuda/src/kernels/kCalculateAmoebaCudaMutualInducedAndGkFields.cu
View file @ 12680294
......@@ -756,9 +756,10 @@ static void cudaComputeAmoebaMutualInducedAndGkFieldBySOR( amoebaGpuContext amoe
// ---------------------------------------------------------------------------------------
static int timestep = 0;
static int timestep = 0;
timestep++;
static const char* methodName = "cudaComputeAmoebaMutualInducedAndGkFieldBySOR";
static const char* methodName = "cudaComputeAmoebaMutualInducedAndGkFieldBySOR";
static double iterationStat[6] = { 0.0, 0.0, 1000.0, 0.0, 0.0, 0.0 };
#ifdef AMOEBA_DEBUG
std::vector<int> fileId;
fileId.resize( 2 );
......@@ -981,9 +982,24 @@ time_t start = clock();
amoebaGpu->mutualInducedConverged = ( !done || iteration > amoebaGpu->mutualInducedMaxIterations ) ? 0 : 1;
if( amoebaGpu->log ){
(void) fprintf( amoebaGpu->log, "%s done=%d converged=%d iteration=%d eps=%14.7e\n",
methodName, done, amoebaGpu->mutualInducedConverged, iteration, amoebaGpu->mutualInducedCurrentEpsilon );
(void) fflush( amoebaGpu->log );
static int count = 0;
count++;
double interationD = static_cast<double>(iteration);
iterationStat[0] += interationD;
iterationStat[1] += interationD*interationD;
iterationStat[2] = interationD < iterationStat[2] ? interationD : iterationStat[2];
iterationStat[3] = interationD > iterationStat[3] ? interationD : iterationStat[3];
iterationStat[4] += 1.0;
if( count == 100 ){
double average = iterationStat[0]/iterationStat[4];
double stddev = iterationStat[1] - average*average*iterationStat[4];
stddev = sqrt( stddev )/(iterationStat[4]-1.0);
(void) fprintf( amoebaGpu->log, "%s iteration=%10.3f stddev=%10.3f min/max[%10.3f %10.3f] %10.1f eps=%14.7e\n",
methodName, average, stddev, iterationStat[2], iterationStat[3], iterationStat[4], amoebaGpu->mutualInducedCurrentEpsilon );
(void) fflush( amoebaGpu->log );
iterationStat[0] = iterationStat[1] = iterationStat[4] = 0.0;
count = 0;
}
}
#ifdef AMOEBA_DEBUG
......
plugins/amoeba/platforms/cuda/tests/AmoebaTinkerParameterFile.cpp
View file @ 12680294
......@@ -88,7 +88,6 @@ static char* strsepLocal( char** lineBuffer, const char* delimiter ){
} while( sc != 0 );
}
}
/**---------------------------------------------------------------------------------------
Tokenize a string
......@@ -128,6 +127,31 @@ printf( "%c", *endOfLine ); fflush( stdout );
return (int) tokenArray.size();
}
/**---------------------------------------------------------------------------------------
Tokenize a string
@param lineBuffer string to tokenize
@param tokenArray upon return vector of tokens
@param delimiter token delimter
@return number of tokens
--------------------------------------------------------------------------------------- */
int tokenizeStringFromLineString( std::string& line, StringVector& tokenArray, const std::string delimiter ){
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nSimTKOpenMMUtilities::tokenizeString";
// ---------------------------------------------------------------------------------------
char buffer[4096];
(void) strcpy( buffer, line.c_str() );
return tokenizeString( buffer, tokenArray, delimiter );
}
/**---------------------------------------------------------------------------------------
* Set field if in map
*
......@@ -801,7 +825,9 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
if( useOpenMMUnits ){
double cubic = bondForce->getAmoebaGlobalHarmonicBondCubic()/AngstromToNm;
double quartic = bondForce->getAmoebaGlobalHarmonicBondQuartic()/AngstromToNm*AngstromToNm;
double quartic = bondForce->getAmoebaGlobalHarmonicBondQuartic()/(AngstromToNm*AngstromToNm);
//double cubic = bondForce->getAmoebaGlobalHarmonicBondCubic();
//double quartic = bondForce->getAmoebaGlobalHarmonicBondQuartic();
bondForce->setAmoebaGlobalHarmonicBondCubic( cubic );
bondForce->setAmoebaGlobalHarmonicBondQuartic( quartic );
......@@ -822,7 +848,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
int particle1, particle2;
double length, k;
bondForce->getBondParameters( ii, particle1, particle2, length, k );
(void) fprintf( log, "%8d %8d %8d %15.7e %15.7e %15.7e %15.7e\n", ii, particle1, particle2, length, k, cubic, quartic);
(void) fprintf( log, "%8d %8d %8d %15.7e %15.7e\n", ii, particle1, particle2, length, k );
// skip to end
......@@ -4587,6 +4613,112 @@ Context* createContext( const std::string& amoebaTinkerParameterFileName, MapStr
}
void checkIntermediateStatesUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap,
int useOpenMMUnits, MapStringString& inputArgumentMap,
FILE* summaryFile, FILE* log ) {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "checkIntermediateStatesUsingAmoebaTinkerParameterFile";
std::string statesFileName = "states.txt";
// ---------------------------------------------------------------------------------------
setStringFromMap( inputArgumentMap, "states", statesFileName);
StringVector forceList;
std::string activeForceNames;
for( MapStringInt::const_iterator ii = forceMap.begin(); ii != forceMap.end(); ii++ ){
if( ii->second ){
forceList.push_back( ii->first );
activeForceNames += ii->first + ":";
}
}
if( forceList.size() >= 11 ){
activeForceNames =ALL_FORCES;
}
MapStringVec3 tinkerForces;
MapStringDouble tinkerEnergies;
MapStringVectorOfVectors supplementary;
MapStringIntI isPresent = forceMap.find( AMOEBA_GK_FORCE );
bool gkIsActive;
if( isPresent != forceMap.end() && isPresent->second != 0 ){
forceMap[AMOEBA_MULTIPOLE_FORCE] = 1;
gkIsActive = true;
} else {
gkIsActive = false;
}
// read parameters into system and coord/velocities into appropriate arrays
// and create context
Context* context = createContext( amoebaTinkerParameterFileName, forceMap,
useOpenMMUnits, inputArgumentMap, supplementary, tinkerForces, tinkerEnergies, log );
StringVectorVector fileContents;
readFile( statesFileName, fileContents, log );
unsigned int lineIndex = 0;
unsigned int stateIndex = 0;
//fprintf( log, "%8u total lines\n", fileContents.size() );
while( lineIndex < (fileContents.size()-1) ){
/*
fprintf( log, "%8u Line %u state=%u ", lineIndex, fileContents[lineIndex].size(), stateIndex );
for( int ii = 0; ii < fileContents[lineIndex].size(); ii++ ){
fprintf( log, "%s ", fileContents[lineIndex][ii].c_str() );
}
fprintf( log, "\n" ); fflush( log ); */
int numberOfAtoms = atoi( fileContents[lineIndex++][0].c_str() );
stateIndex++;
std::vector<Vec3> coordinates;
coordinates.resize( numberOfAtoms );
int skip = 0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
StringVector& stateTokenArray = fileContents[lineIndex++];
/*
fprintf( log, "%8u xLine %u state=%u ", lineIndex, fileContents[lineIndex-1].size(), stateIndex );
for( int ii = 0; ii < fileContents[lineIndex-1].size(); ii++ ){
fprintf( log, "%s ", fileContents[lineIndex-1][ii].c_str() );
}
fprintf( log, "\n" ); fflush( log ); */
if( stateTokenArray[1] == "nan" || stateTokenArray[2] == "nan" || stateTokenArray[3] == "nan" ){
skip = 1;
} else {
coordinates[ii] = Vec3( atof( stateTokenArray[1].c_str() ),
atof( stateTokenArray[2].c_str() ),
atof( stateTokenArray[3].c_str() ) );
}
}
if( skip ){
(void) fprintf( log, "Skipping state=%u line=%u\n", stateIndex, lineIndex );
} else {
(void) fprintf( log, "State=%u coordinates=%u\n", stateIndex, coordinates.size() );
context->setPositions( coordinates );
State state = context->getState(State::Forces | State::Energy);
System& system = context->getSystem();
//std::vector<Vec3> forces = state.getForces();
//double kineticEnergy = state.getPotentialEnergy();
double potentialEnergy = state.getPotentialEnergy();
if( summaryFile ){
int lastIndex = coordinates.size() - 1;
FILE* filePtr = summaryFile;
(void) fprintf( filePtr, "%8u %15.7e %30s [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n",
stateIndex, potentialEnergy, activeForceNames.c_str(),
coordinates[0][0], coordinates[0][1], coordinates[0][2],
coordinates[lastIndex][0], coordinates[lastIndex][1], coordinates[lastIndex][2] );
(void) fflush( filePtr );
}
}
}
}
void testUsingAmoebaTinkerParameterFile( const std::string& amoebaTinkerParameterFileName, MapStringInt& forceMap,
int useOpenMMUnits, MapStringString& inputArgumentMap,
FILE* summaryFile, FILE* log ) {
......@@ -5443,7 +5575,7 @@ void testEnergyConservation( std::string parameterFileName, MapStringInt& forceM
// check that energy fluctuation is within tolerance
ASSERT_EQUAL_TOL( stddevE, 0.0, energyTolerance );
//ASSERT_EQUAL_TOL( stddevE, 0.0, energyTolerance );
}
......@@ -5489,6 +5621,7 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
int checkForces = 1;
int checkEnergyForceConsistency = 0;
int checkEnergyConservation = 0;
int checkIntermediateStates = 0;
// parse arguments
......@@ -5510,10 +5643,10 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
useOpenMMUnits = atoi( value.c_str() );
} else if( key == "checkEnergyForceConsistency" ){
checkEnergyForceConsistency = atoi( value.c_str() );
//if( checkEnergyForceConsistency )checkForces = 0;
} else if( key == "checkEnergyConservation" ){
checkEnergyConservation = atoi( value.c_str() );
//if( checkEnergyForceConsistency )checkForces = 0;
} else if( key == "checkIntermediateStates" ){
checkIntermediateStates = atoi( value.c_str() );
} else if( key == "log" ){
logControl = atoi( value.c_str() );
} else if( key == ALL_FORCES ){
......@@ -5601,6 +5734,12 @@ int runTestsUsingAmoebaTinkerParameterFile( MapStringString& argumentMap ){
testEnergyConservation( parameterFileName, forceMap, useOpenMMUnits,
inputArgumentMap, log, summaryFile );
} else if( checkIntermediateStates ){
// args:
checkIntermediateStatesUsingAmoebaTinkerParameterFile( parameterFileName, forceMap, useOpenMMUnits,
inputArgumentMap, summaryFile, log );
} else {
// args:
// tolerance
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaForceFromParameterFile.cpp
View file @ 12680294
......@@ -45,21 +45,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
/*
//std::string openmmPluginDirectory = "/cygdrive/c/cygwin/home/friedrim/src/openmm/trunk/OpenMM/bin/release";
std::vector<std::string> pluginDirectories;
pluginDirectories.push_back( "C:\\cygwin\\home\\friedrim\\src\\openmm\\trunk\\OpenMM\\bin\\Release" );
//pluginDirectories.push_back( "C:\\cygwin\\home\\friedrim\\src\\openmm\\trunk\\OpenMM\\bin" );
//pluginDirectories.push_back( "/cygdrive/c/cygwin/home/friedrim/src/openmm/trunk/OpenMM/bin/Release" );
//pluginDirectories.push_back( "/cygdrive/c/cygwin/home/friedrim/src/openmm/trunk/OpenMM/bin" );
for( unsigned int ii = 0; ii < pluginDirectories.size(); ii++ ){
std::string openmmPluginDirectory = pluginDirectories[ii];
std::cout << "Plugin directory: " << openmmPluginDirectory << std::endl;
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
}
*/
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
if( numberOfArguments > 1 ){
MapStringString argumentMap;
appendInputArgumentsToArgumentMap( numberOfArguments, argv, argumentMap );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicAngleForce.cpp
View file @ 12680294
......@@ -294,8 +294,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = fopen( "AmoebaHarmonicAngleForce.log", "w" );;
testOneAngle( log );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicBondForce.cpp
View file @ 12680294
......@@ -200,8 +200,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = stderr;
testOneBond( log );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp
View file @ 12680294
......@@ -371,8 +371,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = fopen( "AmoebaHarmonicInPlaneAngleForce.log", "w" );;
testOneAngle( NULL );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaOutOfPlaneBendForce.cpp
View file @ 12680294
......@@ -493,8 +493,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = stderr;
FILE* log = fopen( "AmoebaOutOfPlaneBendForce1.log", "w" );;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPiTorsionForce.cpp
View file @ 12680294
......@@ -302,8 +302,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = stderr;
FILE* log = fopen( "AmoebaPiTorsionForce1.log", "w" );;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaStretchBendForce.cpp
View file @ 12680294
......@@ -284,8 +284,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = stderr;
FILE* log = fopen( "AmoebaStretchBendForce1.log", "w" );;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionForce.cpp
View file @ 12680294
......@@ -331,8 +331,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = stderr;
FILE* log = fopen( "AmoebaTorsionForce1.log", "w" );;
testOneTorsion( log );
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaTorsionTorsionForce.cpp
View file @ 12680294
......@@ -305,8 +305,7 @@ int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "Running test..." << std::endl;
std::string openmmPluginDirectory = "/home/friedrim/src/openmm/trunk/OpenMM/bin";
Platform::loadPluginsFromDirectory( openmmPluginDirectory );
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = stderr;
//FILE* log = fopen( "AmoebaTorsionTorsionForce1.log", "w" );;
......
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