kCalculateAmoebaCudaRotateFrame.cu 21.3 KB
Newer Older
Mark Friedrichs's avatar
Mark Friedrichs committed
1
2
3
4
//-----------------------------------------------------------------------------------------

//-----------------------------------------------------------------------------------------

Mark Friedrichs's avatar
Mark Friedrichs committed
5
#include "cudaKernels.h"
Mark Friedrichs's avatar
Mark Friedrichs committed
6
#include "amoebaCudaKernels.h"
Mark Friedrichs's avatar
Mark Friedrichs committed
7
#include "kCalculateAmoebaCudaUtilities.h"
Mark Friedrichs's avatar
Mark Friedrichs committed
8
9
10
11
12
13
14
15
16
17

#include <stdio.h>
#include <cuda.h>
#include <cstdlib>
using namespace std; 

#define SQRT sqrtf

static __constant__ cudaGmxSimulation cSim;
static __constant__ cudaAmoebaGmxSimulation cAmoebaSim;
18
extern __global__ void kFindInteractionsWithinBlocksPeriodic_kernel(unsigned int*);
Mark Friedrichs's avatar
Mark Friedrichs committed
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39

void SetCalculateAmoebaMultipoleForcesSim(amoebaGpuContext amoebaGpu)
{
    cudaError_t status;
    gpuContext gpu = amoebaGpu->gpuContext;
    status         = cudaMemcpyToSymbol(cSim, &gpu->sim, sizeof(cudaGmxSimulation));     
    RTERROR(status, "SetCalculateAmoebaMultipoleForcesSim: cudaMemcpyToSymbol: SetSim copy to cSim failed");
    status         = cudaMemcpyToSymbol(cAmoebaSim, &amoebaGpu->amoebaSim, sizeof(cudaAmoebaGmxSimulation));     
    RTERROR(status, "SetCalculateAmoebaMultipoleForcesSim: cudaMemcpyToSymbol: SetSim copy to cAmoebaSim failed");
}

void GetCalculateAmoebaMultipoleForcesSim(amoebaGpuContext amoebaGpu)
{
    cudaError_t status;
    gpuContext gpu = amoebaGpu->gpuContext;
    status = cudaMemcpyFromSymbol(&gpu->sim, cSim, sizeof(cudaGmxSimulation));     
    RTERROR(status, "GetCalculateAmoebaMultipoleForcesSim: cudaMemcpyFromSymbol: SetSim copy from cSim failed");
    status = cudaMemcpyFromSymbol(&amoebaGpu->amoebaSim, cAmoebaSim, sizeof(cudaAmoebaGmxSimulation));     
    RTERROR(status, "GetCalculateAmoebaMultipoleForcesSim: cudaMemcpyFromSymbol: SetSim copy from cAmoebaSim failed");
}

40
__device__ static float normVector3( float* vector )
Mark Friedrichs's avatar
Mark Friedrichs committed
41
42
43
44
45
46
47
48
49
50
51
52
53
{

    float norm                    = DOT3( vector, vector );
    float returnNorm              = SQRT( norm );
    norm                          = returnNorm > 0.0f ? 1.0f/returnNorm : 0.0f;

    vector[0]                    *= norm;
    vector[1]                    *= norm;
    vector[2]                    *= norm;

    return returnNorm;
}

Mark Friedrichs's avatar
Mark Friedrichs committed
54
55
#undef AMOEBA_DEBUG

56
57
58
59
60
61
// ZThenX     == 0
// Bisector   == 1
// ZBisect    == 2
// ThreeFold  == 3
// ZOnly      == 4
// NoAxisType == 5
62

Mark Friedrichs's avatar
Mark Friedrichs committed
63
64
65
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_THREADS_PER_BLOCK, 1)
66
#elif (__CUDA_ARCH__ >= 120)
Mark Friedrichs's avatar
Mark Friedrichs committed
67
68
69
70
__launch_bounds__(GT2XX_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_THREADS_PER_BLOCK, 1)
#endif
71
void kCudaComputeCheckChiral_kernel( void )
Mark Friedrichs's avatar
Mark Friedrichs committed
72
73
{

74
75
76
77
78
79
    const int AD          = 0;
    const int BD          = 1;
    const int CD          = 2;
    const int C           = 3;
    float delta[4][3];
 
80
81
    float4* particleCoord        = cSim.pPosq;
    int4* multiPoleParticles     = cAmoebaSim.pMultipoleParticlesIdsAndAxisType;
82
83
84
85
86
    float* labFrameDipole        = cAmoebaSim.pLabFrameDipole;
    float* labFrameQuadrupole    = cAmoebaSim.pLabFrameQuadrupole;
 
    // ---------------------------------------------------------------------------------------
 
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
    int particleIndex            = __mul24(blockIdx.x,blockDim.x) + threadIdx.x;
    int numberOfParticles        = cSim.atoms;
    while( particleIndex < numberOfParticles )
    { 
        // skip z-then-x
    
        int axisType                     = multiPoleParticles[particleIndex].w; 
        if( axisType != 0 && multiPoleParticles[particleIndex].y >= 0 )
        {
     
            // ---------------------------------------------------------------------------------------
         
            int particleA                = particleIndex;
            int particleB                = multiPoleParticles[particleIndex].z;
            int particleC                = multiPoleParticles[particleIndex].x;
            int particleD                = multiPoleParticles[particleIndex].y;
        
            delta[AD][0]                 = particleCoord[particleA].x - particleCoord[particleD].x;
            delta[AD][1]                 = particleCoord[particleA].y - particleCoord[particleD].y;
            delta[AD][2]                 = particleCoord[particleA].z - particleCoord[particleD].z;
        
            delta[BD][0]                 = particleCoord[particleB].x - particleCoord[particleD].x;
            delta[BD][1]                 = particleCoord[particleB].y - particleCoord[particleD].y;
            delta[BD][2]                 = particleCoord[particleB].z - particleCoord[particleD].z;
        
            delta[CD][0]                 = particleCoord[particleC].x - particleCoord[particleD].x;
            delta[CD][1]                 = particleCoord[particleC].y - particleCoord[particleD].y;
            delta[CD][2]                 = particleCoord[particleC].z - particleCoord[particleD].z;
        
            delta[C][0]                  = delta[BD][1]*delta[CD][2] - delta[BD][2]*delta[CD][1];
            delta[C][1]                  = delta[CD][1]*delta[AD][2] - delta[CD][2]*delta[AD][1];
            delta[C][2]                  = delta[AD][1]*delta[BD][2] - delta[AD][2]*delta[BD][1];
         
            float volume                 = delta[C][0]*delta[AD][0] + delta[C][1]*delta[BD][0] + delta[C][2]*delta[CD][0];
            if( volume < 0.0 ){
                labFrameDipole[particleIndex*3+1]            *= -1.0f; // pole(3,i)
                labFrameQuadrupole[particleIndex*9+1]        *= -1.0f; // pole(6,i)  && pole(8,i)
                labFrameQuadrupole[particleIndex*9+3]        *= -1.0f; // pole(10,i) && pole(12,i)
                labFrameQuadrupole[particleIndex*9+5]        *= -1.0f; // pole(6,i)  && pole(8,i)
                labFrameQuadrupole[particleIndex*9+7]        *= -1.0f; // pole(10,i) && pole(12,i)
            }
        }
    
        particleIndex                += gridDim.x*blockDim.x;
    }    
132
}
Mark Friedrichs's avatar
Mark Friedrichs committed
133

134
135
136
__global__
#if (__CUDA_ARCH__ >= 200)
__launch_bounds__(GF1XX_THREADS_PER_BLOCK, 1)
137
#elif (__CUDA_ARCH__ >= 120)
138
139
140
141
142
143
__launch_bounds__(GT2XX_THREADS_PER_BLOCK, 1)
#else
__launch_bounds__(G8X_THREADS_PER_BLOCK, 1)
#endif
void kCudaComputeLabFrameMoments_kernel( void )
{
Mark Friedrichs's avatar
Mark Friedrichs committed
144

145
146
147
148
    float vectorX[3];
    float vectorY[3];
    float vectorZ[3];
 
149
150
151
152
153
    int particleIndex            = __mul24(blockIdx.x,blockDim.x) + threadIdx.x;
    int numberOfParticles        = cSim.atoms;

    float4* particleCoord        = cSim.pPosq;
    int4* multiPoleParticles     = cAmoebaSim.pMultipoleParticlesIdsAndAxisType;
154
155
156
157
158
159
160
161
162
163
164
    float* labFrameDipole        = cAmoebaSim.pLabFrameDipole;
    float* labFrameQuadrupole    = cAmoebaSim.pLabFrameQuadrupole;
 
    // get coordinates of this atom and the z & x axis atoms
    // compute the vector between the atoms and 1/sqrt(d2), d2 is distance between
    // this atom and the axis atom
 
    // this atom is referred to as the k-atom in notes below
 
    // code common to ZThenX and Bisector
    
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
    while( particleIndex < numberOfParticles )
    {
        float4 coordinatesThisParticle   = particleCoord[particleIndex];
     
        int multipoleParticleIndex       = multiPoleParticles[particleIndex].z;
        float4 coordinatesAxisParticle   = particleCoord[multipoleParticleIndex];
     
        vectorZ[0]                       = coordinatesAxisParticle.x - coordinatesThisParticle.x;
        vectorZ[1]                       = coordinatesAxisParticle.y - coordinatesThisParticle.y;
        vectorZ[2]                       = coordinatesAxisParticle.z - coordinatesThisParticle.z;
          
        multipoleParticleIndex           = multiPoleParticles[particleIndex].x; 
        coordinatesAxisParticle          = particleCoord[multipoleParticleIndex];
     
        vectorX[0]                       = coordinatesAxisParticle.x - coordinatesThisParticle.x;
        vectorX[1]                       = coordinatesAxisParticle.y - coordinatesThisParticle.y;
        vectorX[2]                       = coordinatesAxisParticle.z - coordinatesThisParticle.z;
     
        int axisType                     = multiPoleParticles[particleIndex].w; 
          
        /*
            z-only
               (1) norm z
               (2) select random x
               (3) x = x - (x.z)z
               (4) norm x
    
            z-then-x
               (1) norm z
               (2) norm x (not needed)
               (3) x = x - (x.z)z
               (4) norm x
    
            bisector
               (1) norm z
               (2) norm x 
               (3) z = x + z
               (4) norm z
               (5) x = x - (x.z)z 
               (6) norm x 
    
            z-bisect
               (1) norm z
               (2) norm x 
               (3) norm y 
               (3) x = x + y
               (4) norm x
               (5) x = x - (x.z)z 
               (6) norm x 
214
    
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
            3-fold
               (1) norm z
               (2) norm x 
               (3) norm y 
               (4) z = x + y + z
               (5) norm z
               (6) x = x - (x.z)z 
               (7) norm x 
    
        */
    
        // branch based on axis type
         
        float sum                        = normVector3( vectorZ );
    
        if( axisType == 1 ){
    
            // bisector
            
            sum                     = normVector3( vectorX );
            
            vectorZ[0]             += vectorX[0];
            vectorZ[1]             += vectorX[1];
            vectorZ[2]             += vectorX[2];
       
            sum                     = normVector3( vectorZ );
    
        } else if( axisType == 2 || axisType == 3 ){ 
243
     
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
            // z-bisect
    
            multipoleParticleIndex  = multiPoleParticles[particleIndex].y; 
            coordinatesAxisParticle = particleCoord[multipoleParticleIndex];
            vectorY[0]              = coordinatesAxisParticle.x - coordinatesThisParticle.x;
            vectorY[1]              = coordinatesAxisParticle.y - coordinatesThisParticle.y;
            vectorY[2]              = coordinatesAxisParticle.z - coordinatesThisParticle.z;
    
            sum                     = normVector3( vectorY );
            sum                     = normVector3( vectorX );
    
            if( axisType == 2 ){
    
                vectorX[0]         += vectorY[0];
                vectorX[1]         += vectorY[1];
                vectorX[2]         += vectorY[2];
                sum                 = normVector3( vectorX );
     
            } else { 
     
                // 3-fold
265
        
266
267
268
269
270
271
272
273
274
275
276
277
                vectorZ[0]         += vectorX[0] + vectorY[0];
                vectorZ[1]         += vectorX[1] + vectorY[1];
                vectorZ[2]         += vectorX[2] + vectorY[2];
                sum                 = normVector3( vectorZ );
            }
     
        } else if( axisType >= 4 ){ 
    
            vectorX[0]             = 0.1f;
            vectorX[1]             = 0.1f;
            vectorX[2]             = 0.1f;
        }
278
        
279
280
281
282
283
284
285
286
287
        // x = x - (x.z)z
    
        float dot         = vectorZ[0]*vectorX[0] + vectorZ[1]*vectorX[1] + vectorZ[2]*vectorX[2];
            
        vectorX[0]       -= dot*vectorZ[0];
        vectorX[1]       -= dot*vectorZ[1];
        vectorX[2]       -= dot*vectorZ[2];
         
        sum               = normVector3( vectorX );
288
    
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
        vectorY[0]        = (vectorZ[1]*vectorX[2]) - (vectorZ[2]*vectorX[1]);
        vectorY[1]        = (vectorZ[2]*vectorX[0]) - (vectorZ[0]*vectorX[2]);
        vectorY[2]        = (vectorZ[0]*vectorX[1]) - (vectorZ[1]*vectorX[0]);
     
        // use identity rotation matrix for unrecognized axis types
    
        if( axisType < 0 || axisType > 4 ){
    
            vectorX[0] = 1.0f;
            vectorX[1] = 0.0f;
            vectorX[2] = 0.0f;
    
            vectorY[0] = 0.0f;
            vectorY[1] = 1.0f;
            vectorY[2] = 0.0f;
    
            vectorZ[0] = 0.0f;
            vectorZ[1] = 0.0f;
            vectorZ[2] = 1.0f;
308
309
        }
    
310
311
312
313
        float molDipole[3];
        molDipole[0]                            = labFrameDipole[particleIndex*3];
        molDipole[1]                            = labFrameDipole[particleIndex*3+1];
        molDipole[2]                            = labFrameDipole[particleIndex*3+2];
314
        
315
        // set out-of-range elements to 0.0f
Mark Friedrichs's avatar
Mark Friedrichs committed
316
     
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
        labFrameDipole[particleIndex*3]         = molDipole[0]*vectorX[0] + molDipole[1]*vectorY[0] + molDipole[2]*vectorZ[0];
        labFrameDipole[particleIndex*3+1]       = molDipole[0]*vectorX[1] + molDipole[1]*vectorY[1] + molDipole[2]*vectorZ[1];
        labFrameDipole[particleIndex*3+2]       = molDipole[0]*vectorX[2] + molDipole[1]*vectorY[2] + molDipole[2]*vectorZ[2];
        
        // ---------------------------------------------------------------------------------------
        
        float mPole[3][3];
        unsigned int offset           = particleIndex*9;
        
        mPole[0][0]                   = labFrameQuadrupole[offset];
        mPole[0][1]                   = labFrameQuadrupole[offset+1];
        mPole[0][2]                   = labFrameQuadrupole[offset+2];
    
        mPole[1][0]                   = labFrameQuadrupole[offset+3];
        mPole[1][1]                   = labFrameQuadrupole[offset+4];
        mPole[1][2]                   = labFrameQuadrupole[offset+5];
    
        mPole[2][0]                   = labFrameQuadrupole[offset+6];
        mPole[2][1]                   = labFrameQuadrupole[offset+7];
        mPole[2][2]                   = labFrameQuadrupole[offset+8];
    
        labFrameQuadrupole[offset+8]  = vectorX[2]*(vectorX[2]*mPole[0][0] + vectorY[2]*mPole[0][1] + vectorZ[2]*mPole[0][2]);
        labFrameQuadrupole[offset+8] += vectorY[2]*(vectorX[2]*mPole[1][0] + vectorY[2]*mPole[1][1] + vectorZ[2]*mPole[1][2]);
        labFrameQuadrupole[offset+8] += vectorZ[2]*(vectorX[2]*mPole[2][0] + vectorY[2]*mPole[2][1] + vectorZ[2]*mPole[2][2]);
Mark Friedrichs's avatar
Mark Friedrichs committed
341

342
343
344
        labFrameQuadrupole[offset+4]  = vectorX[1]*(vectorX[1]*mPole[0][0] + vectorY[1]*mPole[0][1] + vectorZ[1]*mPole[0][2]);
        labFrameQuadrupole[offset+4] += vectorY[1]*(vectorX[1]*mPole[1][0] + vectorY[1]*mPole[1][1] + vectorZ[1]*mPole[1][2]);
        labFrameQuadrupole[offset+4] += vectorZ[1]*(vectorX[1]*mPole[2][0] + vectorY[1]*mPole[2][1] + vectorZ[1]*mPole[2][2]);
Mark Friedrichs's avatar
Mark Friedrichs committed
345

346
347
348
        labFrameQuadrupole[offset+5]  = vectorX[1]*(vectorX[2]*mPole[0][0] + vectorY[2]*mPole[0][1] + vectorZ[2]*mPole[0][2]);
        labFrameQuadrupole[offset+5] += vectorY[1]*(vectorX[2]*mPole[1][0] + vectorY[2]*mPole[1][1] + vectorZ[2]*mPole[1][2]);
        labFrameQuadrupole[offset+5] += vectorZ[1]*(vectorX[2]*mPole[2][0] + vectorY[2]*mPole[2][1] + vectorZ[2]*mPole[2][2]);
Mark Friedrichs's avatar
Mark Friedrichs committed
349

350
351
352
        labFrameQuadrupole[offset]    = vectorX[0]*(vectorX[0]*mPole[0][0] + vectorY[0]*mPole[0][1] + vectorZ[0]*mPole[0][2]);
        labFrameQuadrupole[offset]   += vectorY[0]*(vectorX[0]*mPole[1][0] + vectorY[0]*mPole[1][1] + vectorZ[0]*mPole[1][2]);
        labFrameQuadrupole[offset]   += vectorZ[0]*(vectorX[0]*mPole[2][0] + vectorY[0]*mPole[2][1] + vectorZ[0]*mPole[2][2]);
Mark Friedrichs's avatar
Mark Friedrichs committed
353

354
355
356
        labFrameQuadrupole[offset+1]  = vectorX[0]*(vectorX[1]*mPole[0][0] + vectorY[1]*mPole[0][1] + vectorZ[1]*mPole[0][2]);
        labFrameQuadrupole[offset+1] += vectorY[0]*(vectorX[1]*mPole[1][0] + vectorY[1]*mPole[1][1] + vectorZ[1]*mPole[1][2]);
        labFrameQuadrupole[offset+1] += vectorZ[0]*(vectorX[1]*mPole[2][0] + vectorY[1]*mPole[2][1] + vectorZ[1]*mPole[2][2]);
Mark Friedrichs's avatar
Mark Friedrichs committed
357

358
359
360
        labFrameQuadrupole[offset+2]  = vectorX[0]*(vectorX[2]*mPole[0][0] + vectorY[2]*mPole[0][1] + vectorZ[2]*mPole[0][2]);
        labFrameQuadrupole[offset+2] += vectorY[0]*(vectorX[2]*mPole[1][0] + vectorY[2]*mPole[1][1] + vectorZ[2]*mPole[1][2]);
        labFrameQuadrupole[offset+2] += vectorZ[0]*(vectorX[2]*mPole[2][0] + vectorY[2]*mPole[2][1] + vectorZ[2]*mPole[2][2]);
361
 
362
363
364
        labFrameQuadrupole[offset+3]  = labFrameQuadrupole[offset+1];
        labFrameQuadrupole[offset+6]  = labFrameQuadrupole[offset+2];
        labFrameQuadrupole[offset+7]  = labFrameQuadrupole[offset+5];
Mark Friedrichs's avatar
Mark Friedrichs committed
365

366
        particleIndex                += gridDim.x*blockDim.x;
367
    }
368
     
Mark Friedrichs's avatar
Mark Friedrichs committed
369
370
371
372
373
374
375
376
377
378
379
380
381
}

void cudaComputeAmoebaLabFrameMoments( amoebaGpuContext amoebaGpu )
{

   // ---------------------------------------------------------------------------------------

   static const char* methodName = "computeCudaAmoebaLabFrameMoments";

   // ---------------------------------------------------------------------------------------

    gpuContext gpu    = amoebaGpu->gpuContext;

382
383
    int numBlocks     = gpu->sim.blocks;
    int numThreads    = gpu->sim.update_threads_per_block;
Mark Friedrichs's avatar
Mark Friedrichs committed
384
385
386
387
388
389
390
391
392
393
394

//#define AMOEBA_DEBUG  
#ifdef AMOEBA_DEBUG
    if( 0 && amoebaGpu->log ){
        (void) fprintf( amoebaGpu->log, "%s: numBlocks/atoms=%d\n", methodName, numBlocks ); (void) fflush( amoebaGpu->log );
        amoebaGpu->psMultipoleParticlesIdsAndAxisType->Download();
        amoebaGpu->psMolecularDipole->Download();
        gpu->psPosq4->Download();
        for( int ii = 0; ii < gpu->natoms; ii++ ){
            int mIndex = 3*ii;
             (void) fprintf( amoebaGpu->log,"%6d [%6d %6d %6d] x[%16.9e %16.9e %16.9e] dpl[%16.9e %16.9e %16.9e]\nRot[%16.9e %16.9e %16.9e] [%16.9e %16.9e %16.9e] [%16.9e %16.9e %16.9e]\n\n", ii,
Mark Friedrichs's avatar
Mark Friedrichs committed
395
396
397
398
399
400
401
402
403
                             amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysData[ii].x,
                             amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysData[ii].y,
                             amoebaGpu->psMultipoleParticlesIdsAndAxisType->_pSysData[ii].w,
                             gpu->psPosq4->_pSysData[ii].x,
                             gpu->psPosq4->_pSysData[ii].y,
                             gpu->psPosq4->_pSysData[ii].z,
                             amoebaGpu->psMolecularDipole->_pSysData[mIndex],
                             amoebaGpu->psMolecularDipole->_pSysData[mIndex+1],
                             amoebaGpu->psMolecularDipole->_pSysData[mIndex+2] );
Mark Friedrichs's avatar
Mark Friedrichs committed
404
            if( ii == 30 )ii = gpu->natoms - 30;
Mark Friedrichs's avatar
Mark Friedrichs committed
405
406
407
408
409
410
        }
    }
//    int64 kernelTime = AmoebaTiming::getTimeOfDay();
    double kernelTime = 0.0;
#endif

411
412
413
414
415
416
417
    // copy molecular moments to lab frame moment arrays
    // check if chiral center requires moments to have sign flipped
    // compute lab frame moments

    cudaMemcpy( amoebaGpu->psLabFrameDipole->_pDevData,      amoebaGpu->psMolecularDipole->_pDevData,    3*gpu->sim.paddedNumberOfAtoms*sizeof( float ), cudaMemcpyDeviceToDevice ); 
    cudaMemcpy( amoebaGpu->psLabFrameQuadrupole->_pDevData, amoebaGpu->psMolecularQuadrupole->_pDevData, 9*gpu->sim.paddedNumberOfAtoms*sizeof( float ), cudaMemcpyDeviceToDevice ); 

418
419
420
421
    kCudaComputeCheckChiral_kernel<<< numBlocks, numThreads>>> ( );
    LAUNCHERROR("kCudaComputeCheckChiral");

    kCudaComputeLabFrameMoments_kernel<<< numBlocks, numThreads>>> ( );
Mark Friedrichs's avatar
Mark Friedrichs committed
422
423
424
425
426
427
428
429
430
431
432
433
    LAUNCHERROR(methodName);

}

void kCalculateAmoebaMultipoleForces(amoebaGpuContext amoebaGpu, bool hasAmoebaGeneralizedKirkwood ) 
{
    std::string methodName = "kCalculateAmoebaMultipoleForces";

    // compute lab frame moments

    cudaComputeAmoebaLabFrameMoments( amoebaGpu );

434
    if( 1 ){
Mark Friedrichs's avatar
Mark Friedrichs committed
435
436
437
438
        gpuContext gpu                       = amoebaGpu->gpuContext;
        std::vector<int> fileId;
        //fileId.push_back( 0 );
        VectorOfDoubleVectors outputVector;
439
440
441
        //cudaLoadCudaFloat4Array( gpu->natoms, 3, gpu->psPosq4,              outputVector, gpu->psAtomIndex->_pSysData, 1.0f );
        cudaLoadCudaFloatArray( gpu->natoms,  3, amoebaGpu->psLabFrameDipole,     outputVector, gpu->psAtomIndex->_pSysData, 1.0f );
        cudaLoadCudaFloatArray( gpu->natoms,  9, amoebaGpu->psLabFrameQuadrupole, outputVector, gpu->psAtomIndex->_pSysData, 1.0f );
Mark Friedrichs's avatar
Mark Friedrichs committed
442
443
444
        cudaWriteVectorOfDoubleVectorsToFile( "CudaLabMoments", fileId, outputVector );
    }   

Mark Friedrichs's avatar
Mark Friedrichs committed
445
446
447
448
449
450
    // compute fixed E-field and mutual induced field 

    if( hasAmoebaGeneralizedKirkwood ){
        cudaComputeAmoebaFixedEAndGkFields( amoebaGpu );
        cudaComputeAmoebaMutualInducedAndGkField( amoebaGpu );
    } else {
451

452
        if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
453

454
455
            cudaComputeAmoebaFixedEField( amoebaGpu );
            cudaComputeAmoebaMutualInducedField( amoebaGpu );
456

457
        } else {
458

Mark Friedrichs's avatar
Mark Friedrichs committed
459
460
461
462
463
            gpuContext gpu = amoebaGpu->gpuContext;
            kFindBlockBoundsPeriodic_kernel<<<(gpu->psGridBoundingBox->_length+63)/64, 64>>>();
            LAUNCHERROR("kFindBlockBoundsPeriodic");
            kFindBlocksWithInteractionsPeriodic_kernel<<<gpu->sim.interaction_blocks, gpu->sim.interaction_threads_per_block>>>();
            LAUNCHERROR("kFindBlocksWithInteractionsPeriodic");
Mark Friedrichs's avatar
Mark Friedrichs committed
464
            //compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, gpu->sim.pWorkUnit, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
Mark Friedrichs's avatar
Mark Friedrichs committed
465
            compactStream(gpu->compactPlan, gpu->sim.pInteractingWorkUnit, amoebaGpu->psWorkUnit->_pDevData, gpu->sim.pInteractionFlag, gpu->sim.workUnits, gpu->sim.pInteractionCount);
Mark Friedrichs's avatar
Mark Friedrichs committed
466
467
468
            kFindInteractionsWithinBlocksPeriodic_kernel<<<gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block,
                    sizeof(unsigned int)*gpu->sim.nonbond_threads_per_block>>>(gpu->sim.pInteractingWorkUnit);
            LAUNCHERROR("kFindInteractionsWithinBlocksPeriodic");
469

470
            cudaComputeAmoebaPmeFixedEField( amoebaGpu );
471
            cudaComputeAmoebaPmeMutualInducedField( amoebaGpu );
472
        }
Mark Friedrichs's avatar
Mark Friedrichs committed
473
474
475
476
    }

    // check if induce dipole calculation converged -- abort if it did not

477
    if( amoebaGpu->mutualInducedDone == 0 ){
Mark Friedrichs's avatar
Mark Friedrichs committed
478
479
       (void) fprintf( stderr, "%s induced dipole calculation did not converge -- aborting!\n", methodName.c_str() );
       (void) fflush( stderr );
Mark Friedrichs's avatar
Mark Friedrichs committed
480
481
482
483
484
       exit(-1);
    }

    // calculate electrostatic forces

485
486
487
    if( amoebaGpu->multipoleNonbondedMethod == AMOEBA_NO_CUTOFF ){
        cudaComputeAmoebaElectrostatic( amoebaGpu );
    } else {
Mark Friedrichs's avatar
Mark Friedrichs committed
488
        cudaComputeAmoebaPmeElectrostatic( amoebaGpu );
489
    }
Mark Friedrichs's avatar
Mark Friedrichs committed
490
491
492
}

#undef AMOEBA_DEBUG