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#include "SphereHarm.hpp" |
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|
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SphereHarm::SphereHarm( int bandWidth ){ |
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bw = bandWidth; |
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|
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/*** ASSUMING WILL SEMINAIVE ALL ORDERS ***/ |
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cutoff = bw; |
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size = 2*bw; |
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|
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/* allocate memory */ |
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rdata = (double *) fftw_malloc(sizeof(double) * (size * size)); |
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idata = (double *) fftw_malloc(sizeof(double) * (size * size)); |
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rcoeffs = (double *) fftw_malloc(sizeof(double) * (bw * bw)); |
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icoeffs = (double *) fftw_malloc(sizeof(double) * (bw * bw)); |
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weights = (double *) fftw_malloc(sizeof(double) * 4 * bw); |
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seminaive_naive_tablespace = |
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(double *) fftw_malloc(sizeof(double) * |
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(Reduced_Naive_TableSize(bw,cutoff) + |
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Reduced_SpharmonicTableSize(bw,cutoff))); |
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workspace = (double *) fftw_malloc(sizeof(double) * |
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((8 * (bw*bw)) + |
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(7 * bw))); |
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|
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|
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/**** |
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At this point, check to see if all the memory has been |
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allocated. If it has not, there's no point in going further. |
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****/ |
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|
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if ( (rdata == NULL) || (idata == NULL) || |
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(rcoeffs == NULL) || (icoeffs == NULL) || |
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(seminaive_naive_tablespace == NULL) || |
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(workspace == NULL) ) |
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{ |
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perror("Error in allocating memory"); |
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exit( 1 ) ; |
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} |
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|
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//precompute the Legendres |
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fprintf(stdout,"Precomputing the Legendres...\n"); |
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seminaive_naive_table = SemiNaive_Naive_Pml_Table( bw, cutoff, |
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seminaive_naive_tablespace, |
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workspace ); |
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|
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//construct fftw plans using the GURU interface |
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/* forward DCT */ |
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dctPlan = fftw_plan_r2r_1d( 2*bw, weights, rdata, |
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FFTW_REDFT10, FFTW_ESTIMATE ) ; |
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|
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/* |
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fftw "preamble" ; |
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note that this plan places the output in a transposed array |
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*/ |
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rank = 1 ; |
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dims[0].n = 2*bw ; |
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dims[0].is = 1 ; |
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dims[0].os = 2*bw ; |
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howmany_rank = 1 ; |
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howmany_dims[0].n = 2*bw ; |
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howmany_dims[0].is = 2*bw ; |
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howmany_dims[0].os = 1 ; |
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|
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/* forward fft */ |
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fftPlan = fftw_plan_guru_split_dft( rank, dims, |
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howmany_rank, howmany_dims, |
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rdata, idata, |
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workspace, workspace+(4*bw*bw), |
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FFTW_ESTIMATE ); |
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|
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//make the weights |
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makeweights( bw, weights ); |
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} |
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|
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SphereHarm::~SphereHarm(){ |
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//free up memory |
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fftw_destroy_plan( fftPlan ); |
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fftw_destroy_plan( dctPlan ); |
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|
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fftw_free(workspace); |
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fftw_free(seminaive_naive_table); |
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fftw_free(seminaive_naive_tablespace); |
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fftw_free(weights); |
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fftw_free(icoeffs); |
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fftw_free(rcoeffs); |
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fftw_free(idata); |
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fftw_free(rdata); |
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} |
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|
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void SphereHarm::doTransforms(vector<double> gridData){ |
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int i; |
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|
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//load the data |
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for (i=0; i<size*size; i++){ |
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rdata[i] = gridData[i]; |
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//our data is all real, so load the imaginary part with zeros |
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idata[i] = 0.0; |
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} |
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|
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//do the forward spherical transform |
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FST_semi_memo(rdata, idata, |
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rcoeffs, icoeffs, |
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bw, |
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seminaive_naive_table, |
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workspace, |
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0, |
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cutoff, |
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&dctPlan, |
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&fftPlan, |
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weights ); |
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} |
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|
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void SphereHarm::printShapesFileStart(char name[200], char particle[80], |
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double mass, double momInert[3][3]){ |
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ofstream shapes(name); |
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shapes << "begin ShapeInfo\n"; |
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shapes << "#name\t\tmass\tI_xx\tI_yy\tI_zz\n"; |
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shapes << particle << "\t" << mass << "\t" << momInert[0][0] << "\t" |
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<< momInert[1][1] << "\t" << momInert[2][2] << "\n"; |
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shapes << "end ShapeInfo\n"; |
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} |
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|
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void SphereHarm::printToShapesFile(char name[200], int index){ |
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ofstream shapes(name, ios::app); |
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|
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biggest = 0.0; |
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nfuncs = 0; |
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for ( l = 0 ; l < bw ; l++ ) { |
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for (m = 0; m < l+1; m++) { |
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dummy1 = seanindex(m, l, bw); |
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dummy2 = seanindex(-m, l, bw); |
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|
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if (m == 0) { |
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cm = normFactor(l,m)*rcoeffs[dummy1]; |
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sm = normFactor(l,m)*icoeffs[dummy1]; |
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} else { |
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cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
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+ rcoeffs[dummy2]); |
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sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
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- icoeffs[dummy2]); |
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} |
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|
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if (fabs(cm) > biggest) biggest = fabs(cm); |
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if (fabs(sm) > biggest) biggest = fabs(sm); |
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} |
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} |
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for ( l = 0 ; l < bw ; l++ ) { |
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for (m = 0; m < l+1; m++) { |
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dummy1 = seanindex(m, l, bw); |
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dummy2 = seanindex(-m, l, bw); |
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|
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if (m == 0) { |
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cm = normFactor(l,m)*rcoeffs[dummy1]; |
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sm = normFactor(l,m)*icoeffs[dummy1]; |
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} else { |
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cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
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+ rcoeffs[dummy2]); |
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sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
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- icoeffs[dummy2]); |
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} |
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|
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if (fabs(cm) > 0.01 * biggest) nfuncs++; |
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if (fabs(sm) > 0.01 * biggest) nfuncs++; |
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} |
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} |
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|
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switch(index){ |
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case 0:{ |
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shapes << "\nbegin ContactFunctions\n"; |
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shapes << "#l\tm\tsin or cos\tcoeff (Ang)\n"; |
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}; break; |
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case 1:{ |
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shapes << "\nbegin RangeFunctions\n"; |
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shapes << "#l\tm\tsin or cos\tcoeff (Ang)\n"; |
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}; break; |
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case 2:{ |
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shapes << "\nbegin StrengthFunctions\n"; |
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shapes << "#l\tm\tsin or cos\tcoeff (kcal/mol)\n"; |
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}; break; |
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} |
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|
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for ( l = 0 ; l < bw ; l++ ) { |
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for (m = 0; m < l+1; m++) { |
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dummy1 = seanindex(m, l, bw); |
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dummy2 = seanindex(-m, l, bw); |
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|
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if (m == 0) { |
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cm = normFactor(l,m)*rcoeffs[dummy1]; |
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sm = normFactor(l,m)*icoeffs[dummy1]; |
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} else { |
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cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
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+ rcoeffs[dummy2]); |
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sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
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- icoeffs[dummy2]); |
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} |
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|
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if (fabs(cm) > 0.01 * biggest) |
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shapes << l << "\t" << m << "\tcos\t\t" << cm << "\n"; |
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if (fabs(sm) > 0.01 * biggest) |
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shapes << l << "\t" << m << "\tsin\t\t" << sm << "\n"; |
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} |
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} |
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switch(index){ |
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case 0:{ |
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shapes << "end ContactFunctions\n"; |
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}; break; |
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case 1:{ |
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shapes << "end RangeFunctions\n"; |
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}; break; |
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case 2:{ |
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shapes << "end StrengthFunctions\n"; |
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}; break; |
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} |
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} |
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|
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double SphereHarm::normFactor(int L, int M){ |
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// normalization factor: |
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if (L+M > 170){ |
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printf("Warning: A coefficient was omitted because l + m > 170.\n" |
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"\tThe double buffer overflows with factorial calculations\n" |
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"\tof 170 and higher. You should consider using a smaller\n" |
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"\tbandwidth if you aren't okay with the loss of the %i, %i\n" |
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"\tspherical harmonic.\n", L, M); |
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return 0.0; |
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} |
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else |
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return sqrt( (2*L+1)/(4.0*M_PI)*factorialFunc((double)(L-M)) |
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/ factorialFunc(double(L+M)) ); |
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} |
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|
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double SphereHarm::factorialFunc(double n) { |
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if (n < 0.0) return NAN; |
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else { |
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if (n < 2.0) return 1.0; |
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else |
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return n*factorialFunc(n-1.0); |
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} |
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} |
